Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1738/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rgraphviz 2.50.0 (landing page) Kasper Daniel Hansen
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the Rgraphviz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rgraphviz.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: Rgraphviz |
Version: 2.50.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rgraphviz_2.50.0.tar.gz |
StartedAt: 2024-11-20 08:23:54 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 08:24:37 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 43.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Rgraphviz.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rgraphviz_2.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Rgraphviz/DESCRIPTION’ ... OK * this is package ‘Rgraphviz’ version ‘2.50.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rgraphviz’ can be installed ... WARNING Found the following significant warnings: WARNING: `aclocal-1.12' is missing on your system. You should only need it if WARNING: `automake-1.12' is missing on your system. You should only need it if ./ltdl.h:44:27: warning: the address of 'libext' will always evaluate as 'true' [-Waddress] dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] dtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes] dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign] lexer.c:435:33: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign] lexer.c:435:41: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign] lexer.c:527:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] route.c:107:29: warning: argument 4 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=] shortest.c:103:47: warning: argument 2 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=] trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses] patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 4.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.graphviz_build_version’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rgraphviz/libs/Rgraphviz.so’: Found ‘__printf_chk’, possibly from ‘printf’ (C) Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘putchar’, possibly from ‘putchar’ (C) Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘rand’, possibly from ‘rand’ (C) Found ‘srand’, possibly from ‘srand’ (C) Found ‘srand48’, possibly from ‘srand48’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz.Rcheck/00check.log’ for details.
Rgraphviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rgraphviz ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Rgraphviz’ ... ** using staged installation configure: Using bundled Graphviz. configure: Searching for the compilers specified by R. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed configure: Preparing to compile Graphviz. configure: Configuring bundled Graphviz. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... 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(cached) yes checking tkInt.h usability... no checking tkInt.h presence... no checking for tkInt.h... no using /usr/lib/tkConfig.sh checking for connect... yes checking for gethostbyname... yes checking for main in -lXpm... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for X11/Xaw/Text.h... yes checking for main in -lXaw... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for main in -lz... yes checking for deflateBound... no checking for GDK_PIXBUF... yes checking for GTK... yes checking for GTKGL... no checking for GTKGLEXT... no checking for GLADE... no checking for qmake-qt4... no checking for qmake-qt3... no checking for qmake... no checking for sincos... yes checking if FILE struct contains _cnt... no checking if FILE struct contains _r... no checking if FILE struct contains _next... no checking if FILE struct contains _IO_read_end... yes checking if errno externs are declared... no checking if getopt externs are declared... yes checking if intptr_t is declared... yes checking if assert needs __eprintf... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating lib/Makefile config.status: creating lib/cdt/Makefile config.status: creating lib/cdt/libcdt.pc config.status: creating lib/graph/Makefile config.status: creating lib/graph/libgraph.pc config.status: creating lib/rbtree/Makefile config.status: creating lib/pathplan/Makefile config.status: creating lib/pathplan/libpathplan.pc config.status: creating lib/dotgen/Makefile config.status: creating lib/neatogen/Makefile config.status: creating lib/fdpgen/Makefile config.status: creating lib/sparse/Makefile config.status: creating lib/sfdpgen/Makefile config.status: creating lib/osage/Makefile config.status: creating lib/circogen/Makefile config.status: creating lib/twopigen/Makefile config.status: creating lib/patchwork/Makefile config.status: creating lib/pack/Makefile config.status: creating lib/ortho/Makefile config.status: creating lib/common/Makefile config.status: creating lib/vpsc/Makefile config.status: creating lib/gvc/Makefile config.status: creating lib/gvc/libgvc.pc config.status: creating lib/xdot/Makefile config.status: creating lib/xdot/libxdot.pc config.status: creating plugin/Makefile config.status: creating plugin/core/Makefile config.status: creating plugin/dot_layout/Makefile config.status: creating plugin/neato_layout/Makefile config.status: creating graphviz.spec config.status: creating Doxyfile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in libltdl (/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix' 'CC=gcc' 'CXX=g++ -std=gnu++17' 'CFLAGS=-g -O2 -Wall' 'CXXFLAGS=-g -O2 -Wall' 'LDFLAGS=-L/usr/local/lib' '--libdir=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'CPPFLAGS=-I/usr/local/include' 'R_LIBS=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/bbs-3.20-bioc/R/site-library' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking which extension is used for runtime loadable modules... .so checking which variable specifies run-time module search path... LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu checking for library containing dlopen... none required checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for unistd.h... (cached) yes checking for dl.h... no checking for sys/dl.h... no checking for dld.h... no checking for mach-o/dyld.h... no checking for dirent.h... yes checking for closedir... yes checking for opendir... yes checking for readdir... yes checking for strlcat... yes checking for strlcpy... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands ---------------------------------------------------------------- graphviz-2.28.0 will be compiled with the following: options: cgraph: No (disabled by default - experimental) digcola: Yes expat: No (disabled) fontconfig: No (disabled) freetype: No (disabled) glut: No (disabled) gts: No (disabled) ipsepcola: No (disabled by default - C++ portability issues) ltdl: No (disabled) ortho: Yes png: No (disabled) jpeg: No (disabled) sfdp: Yes shared: No (disabled) static: Yes qt: No (qmake not found) commands: dot: Yes (always enabled) neato: Yes (always enabled) fdp: Yes (always enabled) circo: Yes (always enabled) twopi: Yes (always enabled) gvpr: Yes (always enabled) gvmap: Yes (always enabled) lefty: Yes smyrna: No (disabled by default - experimental) gvedit: No (qmake not found) plugin libraries: dot_layout: Yes (always enabled) neato_layout: Yes (always enabled) core: Yes (always enabled) devil: No (disabled) gd: No (disabled) gdiplus: No (disabled by default - Windows only) gdk_pixbuf: Yes ghostscript: No (disabled) glitz: No (disabled by default - incomplete) gtk: Yes lasi: No (disabled) ming: No (disabled by default - incomplete) pangocairo: No (disabled) quartz: No (disabled by default - Mac only) rsvg: No (disabled) visio: No (disabled by default - experimental) xlib: No (disabled or unavailable) language extensions: gv_sharp: No (swig not available) gv_go: No (disabled by default - experimental) gv_guile: No (swig not available) gv_io: No (disabled by default - no swig support yet) gv_java: No (swig not available) gv_lua: No (swig not available) gv_ocaml: No (swig not available) gv_perl: No (swig not available) gv_php: No (swig not available) gv_python: No (swig not available) gv_python23: No (disabled by default - for multiversion installs) gv_python24: No (disabled by default - for multiversion installs) gv_python25: No (disabled by default - for multiversion installs) gv_python26: No (disabled by default - for multiversion installs) gv_python27: No (disabled by default - for multiversion installs) gv_R: No (swig not available) gv_ruby: No (swig not available) gv_tcl: No (swig not available) tcldot: Yes tclpathplan: Yes gdtclft: No (gd not available) tkspline: Yes CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/config/missing --run aclocal-1.12 -I m4 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: aclocal-1.12: command not found WARNING: `aclocal-1.12' is missing on your system. You should only need it if you modified `acinclude.m4' or `configure.ac'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/config/missing --run automake-1.12 --gnu /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: automake-1.12: command not found WARNING: `automake-1.12' is missing on your system. You should only need it if you modified `Makefile.am', `acinclude.m4' or `configure.ac'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoconf aclocal.m4:16: warning: this file was generated for autoconf 2.69. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically 'autoreconf'. configure.ac:185: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:185: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_INIT_AUTOMAKE-invocation ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:599: AM_INIT_AUTOMAKE is expanded from... configure.ac:185: the top level configure.ac:252: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from... aclocal.m4:781: AM_PROG_LEX is expanded from... configure.ac:252: the top level configure.ac:374: warning: The macro `AC_HEADER_TIME' is obsolete. configure.ac:374: You should run autoupdate. ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from... configure.ac:374: the top level configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from... ./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:467: the top level configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from... ./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:467: the top level configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from... ./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5343: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... m4/libtool.m4:796: _LT_LANG_DEFAULT_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:467: the top level configure.ac:2722: warning: The macro `AC_TRY_LINK' is obsolete. configure.ac:2722: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/iconv.m4:22: AM_ICONV_LINK is expanded from... m4/iconv.m4:77: AM_ICONV is expanded from... configure.ac:2722: the top level configure.ac:2722: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.ac:2722: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... m4/iconv.m4:77: AM_ICONV is expanded from... configure.ac:2722: the top level /bin/bash ./config.status --recheck running CONFIG_SHELL=/bin/bash /bin/bash ./configure CC=gcc CXX=g++ -std=gnu++17 CFLAGS=-g -O2 -Wall CXXFLAGS=-g -O2 -Wall LDFLAGS=-L/usr/local/lib --prefix=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix --libdir=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib --includedir=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include --with-cgraph=no --enable-swig=no --enable-static --disable-shared --with-pic --with-libgd=no --disable-ltdl --without-x --without-expat --without-devil --without-rsvg --without-ghostscript --without-visio --without-pangocairo --without-lasi --without-glitz --without-freetype2 --without-fontconfig --without-rpat --without-glut --without-gts --without-png --without-tcl --without-jpeg CPPFLAGS=-I/usr/local/include R_LIBS=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/bbs-3.20-bioc/R/site-library --no-create --no-recursion checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking for flex... flex checking for lex output file root... lex.yy checking for lex library... none needed checking for library containing yywrap... -ll checking whether yytext is a pointer... yes checking for bison... bison -y checking for gawk... (cached) gawk checking whether ln -s works... yes checking for sed... /usr/bin/sed checking for grep... grep checking for sort... sort checking for groff... groff checking for ps2pdf... ps2pdf checking for pstopdf... (cached) ps2pdf checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for tclsh8.6... /usr/bin/tclsh8.6 checking whether gcc and cc understand -c and -o together... yes checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking dependency style of g++ -std=gnu++17... gcc3 checking for gcc... gcc checking whether the compiler supports GNU Objective C... yes checking whether gcc accepts -g... yes checking dependency style of gcc... gcc3 checking for inline... inline checking for windres... no checking for an ANSI C-conforming const... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... grep checking for egrep... grep -E checking for uid_t in sys/types.h... yes checking for stdarg.h... yes checking for stddef.h... yes checking for stddef.h... (cached) yes checking for stdlib.h... (cached) yes checking for stdint.h... (cached) yes checking for malloc.h... yes checking for fcntl.h... yes checking for search.h... yes checking for getopt.h... yes checking for pthread.h... yes checking for values.h... yes checking for float.h... yes checking for limits.h... yes checking for termios.h... yes checking for errno.h... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for fenv.h... yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for setjmp.h... yes checking for sys/time.h... (cached) yes checking for sys/times.h... yes checking for sys/types.h... (cached) yes checking for sys/select.h... yes checking for fpu_control.h... yes checking for sys/fpu.h... no checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking for sys/mman.h... yes checking for sys/ioctl.h... yes checking for sys/inotify.h... yes checking for langinfo.h... yes checking for libintl.h... yes checking for crt_externs.h... no checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for socklen_t... yes checking for bool... yes checking for struct dioattr... no checking for main in -lm... yes checking for feenableexcept... yes checking for fesetenv... yes checking for libgen.h... yes checking for basename in -lgen... no checking for working alloca.h... yes checking for alloca... yes checking for lrand48... yes checking for drand48... yes checking for srand48... yes checking for setmode... no checking for setenv... yes checking for getenv... yes checking for __freadable... yes checking for _sysconf... no checking for getrusage... yes checking for strerror... yes checking for cbrt... no checking for lsqrt... no checking for vsnprintf... yes checking for strtoul... yes checking for strtoll... yes checking for strtoull... yes checking for uname... yes checking for memset... yes checking for nl_langinfo... yes checking for pow... no checking for sqrt... no checking for strchr... yes checking for strdup... yes checking for strerror... (cached) yes checking for strstr... yes checking for _NSGetEnviron... no checking for strcasecmp... yes checking for strncasecmp... yes checking for strcasestr... yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking dependency style of g++ -std=gnu++17... (cached) gcc3 checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for ld used by g++ -std=gnu++17... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++17 static flag -static works... yes checking if g++ -std=gnu++17 supports -c -o file.o... yes checking if g++ -std=gnu++17 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc options needed to detect all undeclared functions... none needed checking which extension is used for runtime loadable modules... .so checking which variable specifies run-time module search path... LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu checking for library containing dlopen... none required checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for ltdl.h... yes checking whether lt_dlinterface_register is declared... yes checking for lt_dladvise_preload in -lltdl... yes checking where to find libltdl headers... checking where to find libltdl library... -lltdl checking for unistd.h... (cached) yes checking for dl.h... no checking for sys/dl.h... no checking for dld.h... no checking for mach-o/dyld.h... no checking for dirent.h... yes checking for closedir... yes checking for opendir... yes checking for readdir... yes checking for strlcat... yes checking for strlcpy... yes checking for X... disabled configure: WARNING: X11 not available. using tcl headers from -I/usr/include/tcl8.6 -I/usr/include/tcl8.6/generic checking for tcl.h... yes using /usr/lib/tclConfig.sh checking for wish8.6... /usr/bin/wish8.6 checking for tk.h... yes checking for tk.h... (cached) yes checking for tkInt.h... no using /usr/lib/tkConfig.sh checking for connect... yes checking for gethostbyname... yes checking for main in -lXpm... yes checking for X11/Intrinsic.h... yes checking for X11/Xaw/Text.h... yes checking for main in -lXaw... yes checking for zlib.h... yes checking for main in -lz... yes checking for deflateBound... no checking for GDK_PIXBUF... yes checking for GTK... yes checking for GTKGL... no checking for GTKGLEXT... no checking for GLADE... no checking for qmake-qt4... no checking for qmake-qt3... no checking for qmake... no checking for sincos... yes checking if FILE struct contains _cnt... no checking if FILE struct contains _r... no checking if FILE struct contains _next... no checking if FILE struct contains _IO_read_end... yes checking if errno externs are declared... no checking if getopt externs are declared... yes checking if intptr_t is declared... yes checking if assert needs __eprintf... no checking that generated files are newer than configure... done configure: creating ./config.status ---------------------------------------------------------------- graphviz-2.28.0 will be compiled with the following: options: cgraph: No (disabled by default - experimental) digcola: Yes expat: No (disabled) fontconfig: No (disabled) freetype: No (disabled) glut: No (disabled) gts: No (disabled) ipsepcola: No (disabled by default - C++ portability issues) ltdl: No (disabled) ortho: Yes png: No (disabled) jpeg: No (disabled) sfdp: Yes shared: No (disabled) static: Yes qt: No (qmake not found) commands: dot: Yes (always enabled) neato: Yes (always enabled) fdp: Yes (always enabled) circo: Yes (always enabled) twopi: Yes (always enabled) gvpr: Yes (always enabled) gvmap: Yes (always enabled) lefty: Yes smyrna: No (disabled by default - experimental) gvedit: No (qmake not found) plugin libraries: dot_layout: Yes (always enabled) neato_layout: Yes (always enabled) core: Yes (always enabled) devil: No (disabled) gd: No (disabled) gdiplus: No (disabled by default - Windows only) gdk_pixbuf: Yes ghostscript: No (disabled) glitz: No (disabled by default - incomplete) gtk: Yes lasi: No (disabled) ming: No (disabled by default - incomplete) pangocairo: No (disabled) quartz: No (disabled by default - Mac only) rsvg: No (disabled) visio: No (disabled by default - experimental) xlib: No (disabled or unavailable) language extensions: gv_sharp: No (swig not available) gv_go: No (disabled by default - experimental) gv_guile: No (swig not available) gv_io: No (disabled by default - no swig support yet) gv_java: No (swig not available) gv_lua: No (swig not available) gv_ocaml: No (swig not available) gv_perl: No (swig not available) gv_php: No (swig not available) gv_python: No (swig not available) gv_python23: No (disabled by default - for multiversion installs) gv_python24: No (disabled by default - for multiversion installs) gv_python25: No (disabled by default - for multiversion installs) gv_python26: No (disabled by default - for multiversion installs) gv_python27: No (disabled by default - for multiversion installs) gv_R: No (swig not available) gv_ruby: No (swig not available) gv_tcl: No (swig not available) tcldot: Yes tclpathplan: Yes gdtclft: No (gd not available) tkspline: Yes /bin/bash ./config.status config.status: creating Makefile config.status: creating lib/Makefile config.status: creating lib/cdt/Makefile config.status: creating lib/cdt/libcdt.pc config.status: creating lib/graph/Makefile config.status: creating lib/graph/libgraph.pc config.status: creating lib/rbtree/Makefile config.status: creating lib/pathplan/Makefile config.status: creating lib/pathplan/libpathplan.pc config.status: creating lib/dotgen/Makefile config.status: creating lib/neatogen/Makefile config.status: creating lib/fdpgen/Makefile config.status: creating lib/sparse/Makefile config.status: creating lib/sfdpgen/Makefile config.status: creating lib/osage/Makefile config.status: creating lib/circogen/Makefile config.status: creating lib/twopigen/Makefile config.status: creating lib/patchwork/Makefile config.status: creating lib/pack/Makefile config.status: creating lib/ortho/Makefile config.status: creating lib/common/Makefile config.status: creating lib/vpsc/Makefile config.status: creating lib/gvc/Makefile config.status: creating lib/gvc/libgvc.pc config.status: creating lib/xdot/Makefile config.status: creating lib/xdot/libxdot.pc config.status: creating plugin/Makefile config.status: creating plugin/core/Makefile config.status: creating plugin/dot_layout/Makefile config.status: creating plugin/neato_layout/Makefile config.status: creating graphviz.spec config.status: creating Doxyfile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoheader) aclocal.m4:16: warning: this file was generated for autoconf 2.69. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically 'autoreconf'. rm -f stamp-h1 touch config.h.in cd . && /bin/bash ./config.status config.h config.status: creating config.h grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h make install-recursive make[1]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz' Making install in libltdl make[2]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl' CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run aclocal-1.12 -I m4 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: aclocal-1.12: command not found WARNING: `aclocal-1.12' is missing on your system. You should only need it if you modified `acinclude.m4' or `configure.ac'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run automake-1.12 --foreign /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: automake-1.12: command not found WARNING: `automake-1.12' is missing on your system. You should only need it if you modified `Makefile.am', `acinclude.m4' or `configure.ac'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoconf aclocal.m4:16: warning: this file was generated for autoconf 2.69. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically 'autoreconf'. configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from... ./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:67: the top level configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... ./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from... ./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:67: the top level /bin/bash ./config.status --recheck running CONFIG_SHELL=/bin/bash /bin/bash ./configure --disable-option-checking --prefix=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix CC=gcc CXX=g++ -std=gnu++17 CFLAGS=-g -O2 -Wall CXXFLAGS=-g -O2 -Wall LDFLAGS=-L/usr/local/lib --libdir=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib --includedir=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include --with-cgraph=no --enable-swig=no --enable-static --disable-shared --with-pic --with-libgd=no --disable-ltdl --without-x --without-expat --without-devil --without-rsvg --without-ghostscript --without-visio --without-pangocairo --without-lasi --without-glitz --without-freetype2 --without-fontconfig --without-rpat --without-glut --without-gts --without-png --without-tcl --without-jpeg CPPFLAGS=-I/usr/local/include R_LIBS=/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/bbs-3.20-bioc/R/site-library --cache-file=/dev/null --srcdir=. --no-create --no-recursion checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking which extension is used for runtime loadable modules... .so checking which variable specifies run-time module search path... LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu checking for gcc options needed to detect all undeclared functions... none needed checking for library containing dlopen... none required checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for unistd.h... (cached) yes checking for dl.h... no checking for sys/dl.h... no checking for dld.h... no checking for mach-o/dyld.h... no checking for dirent.h... yes checking for closedir... yes checking for opendir... yes checking for readdir... yes checking for strlcat... yes checking for strlcpy... yes checking that generated files are newer than configure... done configure: creating ./config.status /bin/bash ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make install-am make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl' /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fPIC -DPIC -o dlopen.o mv -f .deps/dlopen.Tpo .deps/dlopen.Plo /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -module -avoid-version -L/usr/local/lib -o dlopen.la dlopen.lo libtool: link: ar cru .libs/dlopen.a dlopen.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/dlopen.a libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" ) /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c -fPIC -DPIC -o libltdlc_la-preopen.o mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c -fPIC -DPIC -o libltdlc_la-lt__alloc.o mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c -fPIC -DPIC -o libltdlc_la-lt_dlloader.o mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c -fPIC -DPIC -o libltdlc_la-lt_error.o mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c -fPIC -DPIC -o libltdlc_la-ltdl.o In file included from libltdl/lt__private.h:51, from ltdl.c:32: ltdl.c: In function 'try_dlopen': ./ltdl.h:44:27: warning: the address of 'libext' will always evaluate as 'true' [-Waddress] 44 | #define LT_STRLEN(s) (((s) && (s)[0]) ? strlen (s) : 0) | ^ libltdl/lt__alloc.h:38:51: note: in definition of macro 'MALLOC' 38 | #define MALLOC(tp, n) (tp*) lt__malloc((n) * sizeof(tp)) | ^ ltdl.c:1268:59: note: in expansion of macro 'LT_STRLEN' 1268 | archive_name = MALLOC (char, LT_STRLEN (name) + LT_STRLEN (libext) + 2); | ^~~~~~~~~ mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c -fPIC -DPIC -o libltdlc_la-slist.o mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -no-undefined -dlpreopen dlopen.la -L/usr/local/lib -o libltdlc.la libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT libtool: link: (cd .libs && gcc -g -O2 -Wall -c -fno-builtin -fPIC -DPIC "libltdlcS.c") libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT" libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a") libtool: link: ar cru .libs/libltdlc.a libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o .libs/libltdlcS.o .libs/libltdlc.lax/dlopen.a/dlopen.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libltdlc.a libtool: link: rm -fr .libs/libltdlc.lax libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" ) (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoheader) aclocal.m4:16: warning: this file was generated for autoconf 2.69. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically 'autoreconf'. rm -f stamp-h1 touch config-h.in cd . && /bin/bash ./config.status config.h config.status: creating config.h make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl' make[2]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl' Making install in lib make[2]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib' Making install in cdt make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' CC dtclose.lo CC dtdisc.lo dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 13 | static Void_t* dtmemory(dt, addr, size, disc) | ^~~~~~~~ CC dtextract.lo CC dtflatten.lo CC dthash.lo dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 15 | static void dthtab(dt) | ^~~~~~ dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 81 | static Void_t* dthash(dt,obj,type) | ^~~~~~ dthash.c: In function 'dthash': dthash.c:306:34: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized] 306 | (*dt->memoryf)(dt,(Void_t*)r,0,disc); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dthash.c:87:30: note: 'r' was declared here 87 | reg Dtlink_t *t, *r, *p; | ^ CC dtlist.lo dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static Void_t* dtlist(dt, obj, type) | ^~~~~~ CC dtmethod.lo CC dtopen.lo CC dtrenew.lo CC dtrestore.lo CC dtsize.lo dtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static int treecount(e) | ^~~~~~~~~ CC dtstat.lo dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static void dttstat(ds,root,depth,level) | ^~~~~~~ dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 31 | static void dthstat(data, ds, count) | ^~~~~~~ CC dtstrhash.lo CC dttree.lo dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 14 | static Void_t* dttree(dt,obj,type) | ^~~~~~ dttree.c: In function 'dttree': dttree.c:294:43: warning: 'me' may be used uninitialized [-Wmaybe-uninitialized] 294 | me->right = link.left; dttree.c:23:34: note: 'me' was declared here 23 | Dtlink_t *l, *r, *me, link; | ^~ CC dttreeset.lo dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static Dtlink_t* treebalance(list, size) | ^~~~~~~~~~~ CC dtview.lo dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 12 | static Void_t* dtvsearch(dt,obj,type) | ^~~~~~~~~ dtview.c: In function 'dtvsearch': dtview.c:20:30: warning: variable 'lk' set but not used [-Wunused-but-set-variable] 20 | int cmp, lk, sz, ky; | ^~ CC dtwalk.lo dtwalk.c: In function 'dtwalk': dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] 14 | int(* userf)(); | ^~~ CCLD libcdt.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libcdt_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libcdt.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libcdt.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.la libtool: install: /usr/bin/install -c .libs/libcdt.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 cdt.3 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 cdt.3.pdf '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libcdt.pc '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 cdt.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' Making install in graph make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph' CC attribs.lo CC agxbuf.lo CC edge.lo CC graph.lo graph.c: In function 'agclose': graph.c:374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 374 | if (g->attr) | ^~ graph.c:376:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 376 | if (g->didset) | ^~ CC graphio.lo /usr/bin/sed "s/yy/ag/g" < y.tab.h > parser.h CC lexer.lo lexer.c: In function 'scan_token': lexer.c:141:11: warning: comparison between pointer and zero character constant [-Wpointer-compare] 141 | if (p == '\0') | ^~ lexer.c:141:9: note: did you mean to dereference the pointer? 141 | if (p == '\0') | ^ lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign] 147 | return p; | ^ lexer.c: In function 'html_pair': lexer.c:322:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 322 | int rc, depth = 1; | ^~ In file included from lexer.c:20: lexer.c: In function 'aglex': agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ lexer.c:413:36: note: in expansion of macro 'agxbuse' 413 | aglval.str = agstrdup_html(agxbuse(&xb)); | ^~~~~~~ lexer.c:435:33: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign] 435 | LexPtr = scan_token(LexPtr, tbuf); | ^~~~~~ | | | char * lexer.c:136:40: note: expected 'unsigned char *' but argument is of type 'char *' 136 | static char *scan_token(unsigned char *p, unsigned char *token) | ~~~~~~~~~~~~~~~^ lexer.c:435:41: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign] 435 | LexPtr = scan_token(LexPtr, tbuf); | ^~~~ | | | char * lexer.c:136:58: note: expected 'unsigned char *' but argument is of type 'char *' 136 | static char *scan_token(unsigned char *p, unsigned char *token) | ~~~~~~~~~~~~~~~^~~~~ lexer.c: In function 'aglasterr': lexer.c:527:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 527 | fread(buf, sizeof(char), len, agerrout); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC node.lo /usr/bin/sed "s/yy/ag/g" < y.tab.c > parser.c CC parser.lo CC refstr.lo CC trie.lo CCLD libgraph.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgraph_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgraph.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libgraph.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.la libtool: install: /usr/bin/install -c .libs/libgraph.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 graph.3 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 graph.3.pdf '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgraph.pc '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graph.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph' Making install in pathplan make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' CC cvt.lo cvt.c:276:13: warning: 'append_bezier' defined but not used [-Wunused-function] 276 | static void append_bezier(Ppoint_t * bezier) | ^~~~~~~~~~~~~ CC inpoly.lo CC route.lo route.c:107:29: warning: argument 4 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=] 107 | Ppoint_t * evs, Ppolyline_t * output) | ~~~~~~~~~~~^~~ In file included from pathutil.h:20, from route.c:21: pathplan.h:37:39: note: previously declared as an array 'Pvector_t[2]' {aka 'struct Pxy_t[2]'} 37 | Pvector_t endpoint_slopes[2], | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ CC shortest.lo shortest.c:103:47: warning: argument 2 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=] 103 | int Pshortestpath(Ppoly_t * polyp, Ppoint_t * eps, Ppolyline_t * output) | ~~~~~~~~~~~^~~ In file included from pathutil.h:20, from shortest.c:22: pathplan.h:31:59: note: previously declared as an array 'Ppoint_t[2]' {aka 'struct Pxy_t[2]'} 31 | extern int Pshortestpath(Ppoly_t * boundary, Ppoint_t endpoints[2], | ~~~~~~~~~^~~~~~~~~~~~ CC shortestpth.lo CC solvers.lo CC triang.lo CC util.lo CC visibility.lo CCLD libpathplan.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libpathplan_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libpathplan.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libpathplan.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.la libtool: install: /usr/bin/install -c .libs/libpathplan.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pathplan.3 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pathplan.3.pdf '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libpathplan.pc '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' Making install in vpsc make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' Making install in rbtree make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree' CC misc.lo CC red_black_tree.lo CC stack.lo CCLD librbtree_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree' Making install in ortho make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/ortho' CC fPQ.lo CC intset.lo CC maze.lo maze.c: In function 'mkMazeGraph': maze.c:325:20: warning: variable 'ncnt' set but not used [-Wunused-but-set-variable] 325 | int nsides, i, ncnt, maxdeg; | ^~~~ CC ortho.lo ortho.c: In function 'addLoop': ortho.c:461:16: warning: variable 'wt' set but not used [-Wunused-but-set-variable] 461 | double wt; | ^~ ortho.c: In function 'addNodeEdges': ortho.c:497:16: warning: variable 'wt' set but not used [-Wunused-but-set-variable] 497 | double wt; | ^~ In file included from /usr/include/stdio.h:980, from ../../lib/common/types.h:17, from structures.h:17, from sgraph.h:17, from maze.h:17, from ortho.c:31: In function 'fprintf', inlined from 'putSeg' at ortho.c:545:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ortho.c: In function 'putSeg': ortho.c:518:9: note: 's' was declared here 518 | char* s; | ^ In function 'fprintf', inlined from 'putSeg' at ortho.c:545:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ortho.c: In function 'putSeg': ortho.c:518:9: note: 's' was declared here 518 | char* s; | ^ In function 'fprintf', inlined from 'putSeg' at ortho.c:542:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ortho.c: In function 'putSeg': ortho.c:518:9: note: 's' was declared here 518 | char* s; | ^ In function 'fprintf', inlined from 'putSeg' at ortho.c:542:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized] 79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ortho.c: In function 'putSeg': ortho.c:518:9: note: 's' was declared here 518 | char* s; | ^ ortho.c: In function 'orthoEdges': ortho.c:1303:25: warning: 'ps' may be used uninitialized [-Wmaybe-uninitialized] 1303 | if (isInPS (ps,hi,ti)) continue; | ^~~~~~~~~~~~~~~~~ ortho.c:1250:15: note: 'ps' was declared here 1250 | PointSet* ps; | ^~ In function 'convertSPtoRoute', inlined from 'orthoEdges' at ortho.c:1341:25: ortho.c:179:25: warning: 'prevbp.y' may be used uninitialized [-Wmaybe-uninitialized] 179 | else if (prevbp.y > bp1.y) l1 = B_UP; | ^ ortho.c: In function 'orthoEdges': ortho.c:152:22: note: 'prevbp.y' was declared here 152 | pointf bp1, bp2, prevbp; /* bend points */ | ^~~~~~ In function 'convertSPtoRoute', inlined from 'orthoEdges' at ortho.c:1341:25: ortho.c:192:25: warning: 'prevbp.x' may be used uninitialized [-Wmaybe-uninitialized] 192 | else if (prevbp.x > bp1.x) l1 = B_RIGHT; | ^ ortho.c: In function 'orthoEdges': ortho.c:152:22: note: 'prevbp.x' was declared here 152 | pointf bp1, bp2, prevbp; /* bend points */ | ^~~~~~ CC partition.lo partition.c: In function 'traverse_polygon': partition.c:328:7: warning: variable 'do_switch' set but not used [-Wunused-but-set-variable] 328 | int do_switch = FALSE; | ^~~~~~~~~ partition.c:327:7: warning: variable 'retval' set but not used [-Wunused-but-set-variable] 327 | int retval; | ^~~~~~ partition.c: In function 'partition': partition.c:731:9: warning: variable 'nt' set but not used [-Wunused-but-set-variable] 731 | int nt; | ^~ partition.c: In function 'make_new_monotone_poly': partition.c:298:18: warning: 'tp' may be used uninitialized [-Wmaybe-uninitialized] 298 | vp0->vnext[ip] = v1; | ~~~~~~~~~~~~~~~^~~~ partition.c:212:7: note: 'tp' was declared here 212 | int tp, tq; | ^~ partition.c:274:5: warning: 'tq' may be used uninitialized [-Wmaybe-uninitialized] 274 | q = vp1->vpos[iq]; | ~~^~~~~~~~~~~~~~~ partition.c:212:11: note: 'tq' was declared here 212 | int tp, tq; | ^~ partition.c: In function 'monotonate_trapezoids': partition.c:665:10: warning: 'size' may be used uninitialized [-Wmaybe-uninitialized] 665 | return size; | ^~~~ partition.c:620:12: note: 'size' was declared here 620 | int i, size; | ^~~~ CC rawgraph.lo CC sgraph.lo CC trapezoid.lo trapezoid.c:22: warning: "__USE_ISOC99" redefined 22 | #define __USE_ISOC99 | In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from trapezoid.c:19: /usr/include/features.h:347: note: this is the location of the previous definition 347 | # define __USE_ISOC99 1 | trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] 66 | static int newnode() | ^~~~~~~ trapezoid.c: In function 'add_segment': trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable] 437 | int tritop = 0, tribot = 0, is_swapped; | ^~~~~~ trapezoid.c: In function 'add_segment.isra': trapezoid.c:996:3: warning: 'tfirstr' may be used uninitialized [-Wmaybe-uninitialized] 996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ trapezoid.c:434:7: note: 'tfirstr' was declared here 434 | int tfirstr, tlastr, tfirstl, tlastl; | ^~~~~~~ trapezoid.c:996:3: warning: 'tlastr' may be used uninitialized [-Wmaybe-uninitialized] 996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ trapezoid.c:434:16: note: 'tlastr' was declared here 434 | int tfirstr, tlastr, tfirstl, tlastl; | ^~~~~~ CCLD libortho_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/ortho' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/ortho' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/ortho' Making install in sparse make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' CC SparseMatrix.lo SparseMatrix.c: In function 'SparseMatrix_import_binary': SparseMatrix.c:629:48: warning: variable 'iread' set but not used [-Wunused-but-set-variable] 629 | int m, n, nz, nzmax, type, format, property, iread; | ^~~~~ CC general.lo CC BinaryHeap.lo In file included from general.h:21, from BinaryHeap.h:17, from BinaryHeap.c:14: BinaryHeap.c: In function 'BinaryHeap_sanity_check': BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 269 | for (i = 0; i < h->len + IntStack_get_length(h->id_stack); i++) assert(mask[i] =- 1); | ^~~~ CC IntStack.lo CCLD libsparse_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' Making install in patchwork make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork' CC patchwork.lo In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2, inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ patchwork.c: In function 'freeTree': patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free] 231 | cp = cp->rightsib; | ~~~^~~~~~~~~~~~~~ In function 'freeTree', inlined from 'freeTree' at patchwork.c:230:2: patchwork.c:233:5: note: call to 'free' here 233 | free (tp); | ^~~~~~~~~ CC patchworkinit.lo CC tree_map.lo CCLD libpatchwork_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork' Making install in common make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/common' CC arrows.lo arrows.c: In function 'arrowOrthoClip': arrows.c:397:28: warning: 'hlen' may be used uninitialized [-Wmaybe-uninitialized] 397 | else r.y = p.y - hlen; | ~~~~^~~~~~ arrows.c:317:21: note: 'hlen' was declared here 317 | double d, tlen, hlen, maxd; | ^~~~ cat brewer_lib svgcolor_lib ../../lib/common/color_names | LC_ALL=C sort > color_lib gawk -f ../../awk/colortbl.awk color_lib > colortbl.h CC colxlate.lo CC fontmetrics.lo CC args.lo CC memory.lo CC globals.lo /usr/bin/sed "s/yy/html/g" < y.tab.h > htmlparse.h CC htmllex.lo In file included from render.h:47, from htmllex.c:15: htmllex.c: In function 'error_context': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmllex.c:57:35: note: in expansion of macro 'agxbuse' 57 | agerr(AGPREV, "... %s ...\n", agxbuse(state.xb)); | ^~~~~~~ /usr/bin/sed "s/yy/html/g" < y.tab.c > htmlparse.c CC htmlparse.lo In file included from render.h:47, from ../../lib/common/htmlparse.y:16: ../../lib/common/htmlparse.y: In function 'appendFItemList': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:193:25: note: in expansion of macro 'agxbuse' 193 | fi->ti.str = strdup(agxbuse(ag)); | ^~~~~~~ ../../lib/common/htmlparse.y: In function 'htmlparse': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:500:24: note: in expansion of macro 'agxbuse' 500 | if (nonSpace(agxbuse(HTMLstate.str))) { | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:511:24: note: in expansion of macro 'agxbuse' 511 | if (nonSpace(agxbuse(HTMLstate.str))) { | ^~~~~~~ CC htmltable.lo In file included from render.h:47, from htmltable.c:35: htmltable.c: In function 'initAnchor': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmltable.c:299:14: note: in expansion of macro 'agxbuse' 299 | id = agxbuse (&xb); | ^~~~~~~ htmltable.c: In function 'nameOf': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmltable.c:1665:12: note: in expansion of macro 'agxbuse' 1665 | return agxbuse(xb); | ^~~~~~~ htmltable.c: In function 'make_html_label': htmltable.c:1828:12: warning: 'env.g' may be used uninitialized [-Wmaybe-uninitialized] 1828 | g = env.g->root; | ~~~^~ htmltable.c:1809:15: note: 'env' declared here 1809 | htmlenv_t env; | ^~~ CC input.lo input.c: In function 'dotneato_basename': input.c:136:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 136 | while (*s) s++; s--; | ^~~~~ input.c:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 136 | while (*s) s++; s--; | ^ In file included from render.h:47, from input.c:15: input.c: In function 'global_def': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ input.c:200:24: note: in expansion of macro 'agxbuse' 200 | sym = dclfun(NULL, agxbuse (xb), rhs); | ^~~~~~~ CC pointset.lo CC postproc.lo CC routespl.lo CC splines.lo CC psusershape.lo psusershape.c: In function 'user_init': psusershape.c:49:30: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int saw_bb, must_inline, rc; | ^~ In file included from render.h:47, from psusershape.c:20: psusershape.c: In function 'ps_string': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ psusershape.c:303:5: note: in expansion of macro 'agxbputc' 303 | agxbputc (&xb, RPAREN); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ psusershape.c:305:9: note: in expansion of macro 'agxbuse' 305 | s = agxbuse(&xb); | ^~~~~~~ psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 268 | int rc; | ^~ CC timing.lo CC labels.lo labels.c: In function 'xml_url_string': labels.c:561:21: warning: variable 'prev' set but not used [-Wunused-but-set-variable] 561 | char *p, *sub, *prev = NULL; | ^~~~ CC ns.lo CC shapes.lo CC utils.lo utils.c: In function 'chkPort': utils.c:690:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 690 | else | ^~~~ utils.c:692:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 692 | pt.name = s; | ^~ In file included from render.h:47, from utils.c:14: utils.c: In function 'clustNode': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:950:5: note: in expansion of macro 'agxbputc' 950 | agxbputc(xb, ':'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:954:29: note: in expansion of macro 'agxbuse' 954 | cn = agnode(agroot(cg), agxbuse(xb)); | ^~~~~~~ utils.c: In function 'scanEntity': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1359:5: note: in expansion of macro 'agxbputc' 1359 | agxbputc(xb, '&'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1369:5: note: in expansion of macro 'agxbputc' 1369 | agxbputc(xb, '#'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1371:5: note: in expansion of macro 'agxbputc' 1371 | agxbputc(xb, ';'); | ^~~~~~~~ utils.c: In function 'htmlEntityUTF8': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1515:18: note: in expansion of macro 'agxbuse' 1515 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1456:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1456 | int rc; | ^~ utils.c: In function 'latin1ToUTF8': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1555:18: note: in expansion of macro 'agxbuse' 1555 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1531:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1531 | int rc; | ^~ utils.c: In function 'utf8ToLatin1': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1587:18: note: in expansion of macro 'agxbuse' 1587 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1573:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1573 | int rc; | ^~ CC geom.lo CC output.lo In file included from render.h:47, from output.c:14: output.c: In function 'attach_attrs_and_arrows': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:350:29: note: in expansion of macro 'agxbuse' 350 | agset(n, "pos", agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:373:31: note: in expansion of macro 'agxbuse' 373 | agset(n, "rects", agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:391:25: note: in expansion of macro 'agxbputc' 391 | agxbputc(&xb, ' '); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:403:46: note: in expansion of macro 'agxbuse' 403 | agxset(n, N_vertices->index, agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:417:25: note: in expansion of macro 'agxbputc' 417 | agxbputc(&xb, ';'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:434:29: note: in expansion of macro 'agxbputc' 434 | agxbputc(&xb, ' '); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:440:33: note: in expansion of macro 'agxbuse' 440 | agset(e, "pos", agxbuse(&xb)); | ^~~~~~~ CC emit.lo In file included from render.h:47, from emit.c:25: emit.c: In function 'getObjId': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:212:9: note: in expansion of macro 'agxbputc' 212 | agxbputc (xb, '_'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:218:12: note: in expansion of macro 'agxbuse' 218 | return agxbuse(xb); | ^~~~~~~ emit.c: In function 'emit_xdot': emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable] 941 | char* fontname; | ^~~~~~~~ emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable] 940 | double fontsize; | ^~~~~~~~ emit.c: In function 'selectedlayer': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:1152:22: note: in expansion of macro 'agxbuse' 1152 | w1 = w0 = strtok(agxbuse(&xb), gvc->layerDelims); | ^~~~~~~ emit.c: In function 'nodeIntersect': emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable] 2247 | char* target; | ^~~~~~ emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable] 2246 | char* tooltip; | ^~~~~~~ emit.c: In function 'xdotBB': emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable] 2474 | pointf sz; | ^~ emit.c: In function 'style_token': emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 3262 | int token, rc; | ^~ emit.c: In function 'parse_style': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:3356:17: note: in expansion of macro 'agxbputc' 3356 | agxbputc(&ps_xb, '\0'); /* terminate previous */ | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:3359:29: note: in expansion of macro 'agxbuse' 3359 | agxbput(&ps_xb, agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:3360:13: note: in expansion of macro 'agxbputc' 3360 | agxbputc(&ps_xb, '\0'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:3372:11: note: in expansion of macro 'agxbuse' 3372 | (void)agxbuse(&ps_xb); /* adds final '\0' to buffer */ | ^~~~~~~ In file included from /usr/include/stdio.h:980, from types.h:17, from render.h:40: In function 'sprintf', inlined from 'getObjId' at emit.c:215:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: 'idnum' may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ emit.c: In function 'getObjId': emit.c:182:10: note: 'idnum' was declared here 182 | long idnum; | ^~~~~ emit.c:214:5: warning: 'pfx' may be used uninitialized [-Wmaybe-uninitialized] 214 | agxbput (xb, pfx); | ^~~~~~~~~~~~~~~~~ emit.c:183:11: note: 'pfx' was declared here 183 | char* pfx; | ^~~ emit.c: In function 'xdotBB': emit.c:2515:18: warning: 'fontsize' may be used uninitialized [-Wmaybe-uninitialized] 2515 | sz = textsize (g, op->para, fontname, fontsize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:2471:12: note: 'fontsize' was declared here 2471 | double fontsize; | ^~~~~~~~ emit.c:2515:18: warning: 'fontname' may be used uninitialized [-Wmaybe-uninitialized] 2515 | sz = textsize (g, op->para, fontname, fontsize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:2472:11: note: 'fontname' was declared here 2472 | char* fontname; | ^~~~~~~~ In function 'multicolor', inlined from 'emit_edge_graphics' at emit.c:1814:10, inlined from 'emit_edge' at emit.c:2389:2, inlined from 'emit_edge' at emit.c:2350:13: emit.c:1776:13: warning: 'endcolor' may be used uninitialized [-Wmaybe-uninitialized] 1776 | gvrender_set_fillcolor(job, endcolor); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c: In function 'emit_edge': emit.c:1723:11: note: 'endcolor' was declared here 1723 | char* endcolor; | ^~~~~~~~ In function 'emit_edge_graphics', inlined from 'emit_edge' at emit.c:2389:2, inlined from 'emit_edge' at emit.c:2350:13: emit.c:1921:17: warning: 'bz.list' may be used uninitialized [-Wmaybe-uninitialized] 1921 | arrow_gen(job, EMIT_TDRAW, bz.sp, bz.list[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1922 | arrowsize, penwidth, bz.sflag); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c: In function 'emit_edge': emit.c:1792:12: note: 'bz.list' was declared here 1792 | bezier bz; | ^~ In function 'emit_edge_graphics', inlined from 'emit_edge' at emit.c:2389:2, inlined from 'emit_edge' at emit.c:2350:13: emit.c:1932:61: warning: 'bz.size' may be used uninitialized [-Wmaybe-uninitialized] 1932 | arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1], | ~~^~~~~ emit.c: In function 'emit_edge': emit.c:1792:12: note: 'bz.size' was declared here 1792 | bezier bz; | ^~ In function 'emit_edge_graphics', inlined from 'emit_edge' at emit.c:2389:2, inlined from 'emit_edge' at emit.c:2350:13: emit.c:1913:16: warning: 'bz.sflag' may be used uninitialized [-Wmaybe-uninitialized] 1913 | if (bz.sflag) { | ^ emit.c: In function 'emit_edge': emit.c:1792:12: note: 'bz.sflag' was declared here 1792 | bezier bz; | ^~ In function 'emit_edge_graphics', inlined from 'emit_edge' at emit.c:2389:2, inlined from 'emit_edge' at emit.c:2350:13: emit.c:1924:16: warning: 'bz.eflag' may be used uninitialized [-Wmaybe-uninitialized] 1924 | if (bz.eflag) { | ^ emit.c: In function 'emit_edge': emit.c:1792:12: note: 'bz.eflag' was declared here 1792 | bezier bz; | ^~ CCLD libcommon_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/common' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/common' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/common' Making install in pack make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pack' CC ccomps.lo CC pack.lo pack.c: In function 'putGraphs': pack.c:953:12: warning: 'pts' may be used uninitialized [-Wmaybe-uninitialized] 953 | return pts; | ^~~ pack.c:920:12: note: 'pts' was declared here 920 | point* pts; | ^~~ CCLD libpack_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pack' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pack.3 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pack.3.pdf '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pack.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pack' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pack' Making install in xdot make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' CC xdot.lo xdot.c: In function 'sprintXDot': xdot.c:537:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 537 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xdot.c:538:21: note: in expansion of macro 'agxbputc' 538 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ xdot.c:606:16: note: in expansion of macro 'agxbuse' 606 | s = strdup(agxbuse(&xb)); | ^~~~~~~ CCLD libxdot.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libxdot_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libxdot.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libxdot.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.la libtool: install: /usr/bin/install -c .libs/libxdot.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 xdot.3 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 xdot.3.pdf '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libxdot.pc '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 xdot.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' Making install in gvc make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' CC gvrender.lo CC gvlayout.lo CC gvdevice.lo In file included from ../../lib/common/types.h:18, from gvplugin_device.h:17, from gvdevice.c:55: gvdevice.c: In function 'gvfwrite': gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 269 | assert(size = sizeof(char)); | ^~~~ CC gvloadimage.lo CC gvcontext.lo CC gvjobs.lo CC gvevent.lo CC gvplugin.lo In file included from gvplugin.c:23: gvplugin.c: In function 'gvplugin_list': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:392:17: note: in expansion of macro 'agxbputc' 392 | agxbputc(&xb,' '); agxbput(&xb, (*pnext)->typestr); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:393:17: note: in expansion of macro 'agxbputc' 393 | agxbputc(&xb,':'); agxbput(&xb, (*pnext)->package->name); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:410:17: note: in expansion of macro 'agxbputc' 410 | agxbputc(&xb,' '); agxbput(&xb, q); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvplugin.c:423:14: note: in expansion of macro 'agxbuse' 423 | bp = agxbuse(&xb); | ^~~~~~~ CC gvconfig.lo CC gvtextlayout.lo CC gvusershape.lo gvusershape.c: In function 'gvusershape_open': gvusershape.c:415:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 415 | if (!(us->data = (void*)find_user_shape(us->name))) | ^~ gvusershape.c:417:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 417 | free(us); | ^~~~ CC gvc.lo CCLD libgvc.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvc_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvc.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libgvc.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.la libtool: install: /usr/bin/install -c .libs/libgvc.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 gvc.3 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 gvc.3.pdf '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgvc.pc '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' Making install in circogen make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/circogen' CC circularinit.lo CC nodelist.lo CC block.lo CC edgelist.lo CC circular.lo CC deglist.lo CC blocktree.lo CC blockpath.lo CC circpos.lo In function 'positionChildren', inlined from 'position' at circpos.c:421:2, inlined from 'doBlock' at circpos.c:468:6: circpos.c:338:20: warning: 'midAngle' may be used uninitialized [-Wmaybe-uninitialized] 338 | PSI(pi->n) = midAngle; circpos.c: In function 'doBlock': circpos.c:264:39: note: 'midAngle' was declared here 264 | double mindistAngle, rotateAngle, midAngle; | ^~~~~~~~ CC nodeset.lo CCLD libcircogen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/circogen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/circogen' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/circogen' Making install in dotgen make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen' CC acyclic.lo CC class1.lo CC class2.lo CC cluster.lo CC compound.lo CC conc.lo CC decomp.lo CC fastgr.lo CC flat.lo CC dotinit.lo CC mincross.lo In function 'balanceNodes', inlined from 'balance' at mincross.c:506:3, inlined from 'mincross.constprop' at mincross.c:638:6: mincross.c:414:12: warning: 'sepIndex' may be used uninitialized [-Wmaybe-uninitialized] 414 | for (i = sepIndex - 1; i >= 0; i--) { | ~~^~~~~~~~~~~~~~ mincross.c: In function 'mincross.constprop': mincross.c:374:9: note: 'sepIndex' was declared here 374 | int sepIndex; | ^~~~~~~~ CC position.lo CC rank.lo CC sameport.lo CC dotsplines.lo dotsplines.c: In function 'makeLineEdge': dotsplines.c:1604:30: warning: right-hand operand of comma expression has no effect [-Wunused-value] 1604 | lp = ED_label(e)->pos, lp; | ^ dotsplines.c: In function 'completeregularpath': dotsplines.c:1866:9: warning: variable 'pn' set but not used [-Wunused-but-set-variable] 1866 | int pn; | ^~ dotsplines.c:1865:13: warning: variable 'pp' set but not used [-Wunused-but-set-variable] 1865 | pointf *pp; | ^~ dotsplines.c: In function '_dot_splines': dotsplines.c:882:12: warning: 'lminx' may be used uninitialized [-Wmaybe-uninitialized] 882 | double lminx, lmaxx; | ^~~~~ dotsplines.c:882:19: warning: 'lmaxx' may be used uninitialized [-Wmaybe-uninitialized] 882 | double lminx, lmaxx; | ^~~~~ dotsplines.c:488:9: warning: 'edges' may be used uninitialized [-Wmaybe-uninitialized] 488 | free(edges); | ^~~~~~~~~~~ dotsplines.c:268:50: note: 'edges' was declared here 268 | edge_t *e, *e0, *e1, *ea, *eb, *le0, *le1, **edges; | ^~~~~ dotsplines.c:489:15: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized] 489 | free(P->boxes); | ~^~~~~~~ dotsplines.c:269:11: note: 'P' was declared here 269 | path *P; | ^ CC aspect.lo aspect.c: In function 'computeCombiAR': aspect.c:1614:12: warning: variable 'maxLayerIndex' set but not used [-Wunused-but-set-variable] 1614 | int i, maxLayerIndex; | ^~~~~~~~~~~~~ In function 'reduceMaxWidth2', inlined from 'applyPacking2' at aspect.c:1088:5, inlined from 'rank3' at aspect.c:1824:2: aspect.c:737:25: warning: 'maxLayerIndex' may be used uninitialized [-Wmaybe-uninitialized] 737 | layerWidthInfo[maxLayerIndex].nNodeGroupsInLayer, | ^ aspect.c: In function 'rank3': aspect.c:702:9: note: 'maxLayerIndex' was declared here 702 | int maxLayerIndex; | ^~~~~~~~~~~~~ In function 'reduceMaxWidth2', inlined from 'applyPacking2' at aspect.c:1088:5, inlined from 'rank3' at aspect.c:1824:2: aspect.c:749:8: warning: 'nextMaxWidth' may be used uninitialized [-Wmaybe-uninitialized] 749 | if (nextMaxWidth <= layerWidthInfo[maxLayerIndex].width / 4 | ^ aspect.c: In function 'rank3': aspect.c:703:12: note: 'nextMaxWidth' was declared here 703 | double nextMaxWidth; | ^~~~~~~~~~~~ CCLD libdotgen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen' Making install in fdpgen make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen' CC comp.lo CC dbg.lo CC grid.lo CC fdpinit.lo CC layout.lo CC tlayout.lo CC xlayout.lo CC clusteredges.lo CCLD libfdpgen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen' Making install in neatogen make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen' CC adjust.lo adjust.c: In function 'getSizes': adjust.c:674:48: warning: 'nedge_nodes' may be used uninitialized [-Wmaybe-uninitialized] 674 | if (elabels && IS_LNODE(n)) nedge_nodes++; | ~~~~~~~~~~~^~ adjust.c:670:12: note: 'nedge_nodes' was declared here 670 | int i, nedge_nodes; | ^~~~~~~~~~~ adjust.c: In function 'removeOverlapWith': adjust.c:1045:9: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1045 | int ret; | ^~~ CC circuit.lo CC edges.lo CC geometry.lo CC heap.lo CC hedges.lo CC info.lo CC neatoinit.lo CC legal.lo CC lu.lo CC matinv.lo CC memory.lo CC poly.lo CC printvis.lo CC site.lo CC solve.lo CC neatosplines.lo neatosplines.c: In function 'makeObstacle': neatosplines.c:363:13: warning: variable 'desc' set but not used [-Wunused-but-set-variable] 363 | epsf_t *desc; | ^~~~ neatosplines.c: In function '_spline_edges': neatosplines.c:603:15: warning: unused variable 'rtr' [-Wunused-variable] 603 | router_t* rtr = 0; | ^~~ CC stuff.lo CC voronoi.lo voronoi.c: In function 'voronoi': voronoi.c:46:49: warning: 'newintstar.y' may be used uninitialized [-Wmaybe-uninitialized] 45 | if (newsite != (struct Site *) NULL && (PQempty() | ~~~~~~~~~ 46 | || newsite->coord.y < | ^~~~~~~~~~~~~~~~~~~~~ 47 | newintstar.y | ~~~~~~~~~~~~ voronoi.c:26:11: note: 'newintstar.y' was declared here 26 | Point newintstar; | ^~~~~~~~~~ CC stress.lo stress.c: In function 'mdsModel': stress.c:1383:19: warning: 'delta' may be used uninitialized [-Wmaybe-uninitialized] 1383 | delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stress.c:1370:12: note: 'delta' was declared here 1370 | double delta; | ^~~~~ CC kkutils.lo CC matrix_ops.lo CC embed_graph.lo CC dijkstra.lo CC conjgrad.lo CC pca.lo CC closest.lo CC bfs.lo CC constraint.lo CC quad_prog_solve.lo CC smart_ini_x.lo CC constrained_majorization.lo CC opt_arrangement.lo CC overlap.lo CC call_tri.lo CC compute_hierarchy.lo CC delaunay.lo CC multispline.lo CCLD libneatogen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen' Making install in twopigen make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen' CC twopiinit.lo CC circle.lo In function 'getRankseps', inlined from 'setAbsolutePos' at circle.c:299:15, inlined from 'circleLayout' at circle.c:368:5: circle.c:285:12: warning: 'delx' may be used uninitialized [-Wmaybe-uninitialized] 285 | xf += delx; | ~~~^~~~~~~ circle.c: In function 'circleLayout': circle.c:268:20: note: 'delx' was declared here 268 | double xf = 0, delx, d; | ^~~~ CCLD libtwopigen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen' Making install in sfdpgen make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen' CC sfdpinit.lo CC spring_electrical.lo spring_electrical.c: In function 'rotate': spring_electrical.c:1850:8: warning: variable 'y' set but not used [-Wunused-but-set-variable] 1850 | real y[4], axis[2], center[2], x0, x1; | ^ CC LinkedList.lo CC sparse_solve.lo CC post_process.lo post_process.c: In function 'StressMajorizationSmoother2_new': post_process.c:110:36: warning: variable 'dd' set but not used [-Wunused-but-set-variable] 110 | real *avg_dist, diag_d, diag_w, *dd, dist, s = 0, stop = 0, sbot = 0; | ^~ post_process.c: In function 'StressMajorizationSmoother_smooth': post_process.c:578:102: warning: variable 'res' set but not used [-Wunused-but-set-variable] 578 | real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.; | ^~~ post_process.c:578:9: warning: variable 'w' set but not used [-Wunused-but-set-variable] 578 | real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.; | ^ post_process.c:577:32: warning: variable 'jw' set but not used [-Wunused-but-set-variable] 577 | int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0; | ^~ post_process.c:577:27: warning: variable 'iw' set but not used [-Wunused-but-set-variable] 577 | int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0; | ^~ post_process.c: In function 'TriangleSmoother_new': post_process.c:698:68: warning: variable 'jd' set but not used [-Wunused-but-set-variable] 698 | int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz; | ^~ post_process.c:698:63: warning: variable 'id' set but not used [-Wunused-but-set-variable] 698 | int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz; | ^~ CC stress_model.lo CC uniform_stress.lo uniform_stress.c: In function 'uniform_stress': uniform_stress.c:112:8: warning: variable 'res' set but not used [-Wunused-but-set-variable] 112 | real res; | ^~~ CC QuadTree.lo CC Multilevel.lo Multilevel.c: In function 'maximal_independent_vertex_set': Multilevel.c:87:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 87 | int i, ii, j, *ia, *ja, m, n, *p = NULL; | ^ Multilevel.c: In function 'maximal_independent_vertex_set_RS': Multilevel.c:138:57: warning: variable 'removed' set but not used [-Wunused-but-set-variable] 138 | int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0; | ^~~~~~~ Multilevel.c:138:48: warning: variable 'n' set but not used [-Wunused-but-set-variable] 138 | int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0; | ^ Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_leaves_first': Multilevel.c:327:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 327 | int i, ii, j, *ia, *ja, m, n, *p = NULL, q; | ^ Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_supernodes_first': Multilevel.c:502:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 502 | int i, ii, j, *ia, *ja, m, n, *p = NULL; | ^ Multilevel.c: In function 'maximal_independent_edge_set_heavest_cluster_pernode_leaves_first': Multilevel.c:646:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 646 | int i, ii, j, *ia, *ja, m, n, *p = NULL, q, iv; | ^ CC PriorityQueue.lo CCLD libsfdpgen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen' Making install in osage make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage' CC osageinit.lo CCLD libosage_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage' make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib' make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib' make[2]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib' Making install in plugin make[2]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin' Making install in core make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core' CC gvplugin_core.lo CC gvrender_core_dot.lo In file included from gvrender_core_dot.c:32: gvrender_core_dot.c: In function 'xdot_str': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:100:5: note: in expansion of macro 'agxbputc' 100 | agxbputc(xbufs[emit_state], ' '); | ^~~~~~~~ gvrender_core_dot.c: In function 'xdot_points': gvrender_core_dot.c:107:12: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 107 | int i, rc; | ^~ gvrender_core_dot.c: In function 'xdot_style': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:162:13: note: in expansion of macro 'agxbputc' 162 | agxbputc(&xbuf, '('); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:166:21: note: in expansion of macro 'agxbputc' 166 | agxbputc(&xbuf, ','); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:172:13: note: in expansion of macro 'agxbputc' 172 | agxbputc(&xbuf, ')'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:174:30: note: in expansion of macro 'agxbuse' 174 | xdot_str (job, "S ", agxbuse(&xbuf)); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_node': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:186:38: note: in expansion of macro 'agxbuse' 186 | agxset(n, xd->n_draw->index, agxbuse(xbufs[EMIT_NDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:192:40: note: in expansion of macro 'agxbuse' 192 | agxset(n, xd->n_l_draw->index, agxbuse(xbufs[EMIT_NLABEL])); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_edge': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:206:38: note: in expansion of macro 'agxbuse' 206 | agxset(e, xd->e_draw->index, agxbuse(xbufs[EMIT_EDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:212:38: note: in expansion of macro 'agxbuse' 212 | agxset(e, xd->t_draw->index, agxbuse(xbufs[EMIT_TDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:218:38: note: in expansion of macro 'agxbuse' 218 | agxset(e, xd->h_draw->index, agxbuse(xbufs[EMIT_HDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:224:39: note: in expansion of macro 'agxbuse' 224 | agxset(e, xd->e_l_draw->index,agxbuse(xbufs[EMIT_ELABEL])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:230:39: note: in expansion of macro 'agxbuse' 230 | agxset(e, xd->tl_draw->index, agxbuse(xbufs[EMIT_TLABEL])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:236:39: note: in expansion of macro 'agxbuse' 236 | agxset(e, xd->hl_draw->index, agxbuse(xbufs[EMIT_HLABEL])); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_cluster': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:289:42: note: in expansion of macro 'agxbuse' 289 | agxset(cluster_g, xd->g_draw->index, agxbuse(xbufs[EMIT_CDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:295:48: note: in expansion of macro 'agxbuse' 295 | agxset(cluster_g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_CLABEL])); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_graph': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:436:38: note: in expansion of macro 'agxbuse' 436 | agxset(g, xd->g_draw->index, agxbuse(xbufs[EMIT_GDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:444:40: note: in expansion of macro 'agxbuse' 444 | agxset(g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_GLABEL])); | ^~~~~~~ CC gvrender_core_fig.lo CC gvrender_core_map.lo CC gvrender_core_ps.lo CC gvrender_core_svg.lo CC gvrender_core_tk.lo gvrender_core_tk.c: In function 'tkgen_print_tags': gvrender_core_tk.c:58:18: warning: variable 'ObjId' set but not used [-Wunused-but-set-variable] 58 | unsigned int ObjId; | ^~~~~ gvrender_core_tk.c:57:21: warning: variable 'ObjPart' set but not used [-Wunused-but-set-variable] 57 | char *ObjType, *ObjPart; | ^~~~~~~ CC gvrender_core_vml.lo gvrender_core_vml.c: In function 'vml_ellipse': gvrender_core_vml.c:452:38: warning: variable 'bottom' set but not used [-Wunused-but-set-variable] 452 | double dx, dy, left, right, top, bottom; | ^~~~~~ gvrender_core_vml.c:452:26: warning: variable 'right' set but not used [-Wunused-but-set-variable] 452 | double dx, dy, left, right, top, bottom; | ^~~~~ CC gvloadimage_core.lo gvloadimage_core.c:19:22: warning: extra tokens at end of #include directive 19 | #include <unistd.h> # for read() declaration | ^ CCLD libgvplugin_core_C.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvplugin_core.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvplugin_core.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core' Making install in dot_layout make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' CC gvplugin_dot_layout.lo CC gvlayout_dot_layout.lo CCLD libgvplugin_dot_layout_C.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvplugin_dot_layout.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvplugin_dot_layout.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' Making install in neato_layout make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' CC gvplugin_neato_layout.lo CC gvlayout_neato_layout.lo CCLD libgvplugin_neato_layout_C.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvplugin_neato_layout.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvplugin_neato_layout.la '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: install: chmod 644 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: install: ranlib /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/sbin" ldconfig -n /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin' make[4]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin' make[2]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin' make[2]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz' make[3]: Entering directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man7' /usr/bin/install -c -m 644 graphviz.7 '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man7' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graphviz_version.h '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/mkdir -p '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc' /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc' make[3]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz' make[2]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz' make[1]: Leaving directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz' cp: -r not specified; omitting directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' cp: -r not specified; omitting directory '/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes checking for deflateBound in -lz... yes checking for library containing pow... -lm checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for whether compiler has bool... yes configure: Using the following compilation and linking flags for Rgraphviz configure: PKG_CFLAGS= -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz configure: PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm configure: GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 configure: Compiling using Graphviz version: '2.28.0'. configure: Using bundled Graphviz: 'TRUE'. configure: creating ./config.status config.status: creating R/graphviz_build_version.R config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function ‘Rgraphviz_agopenSimple’: LL_funcs.c:430:29: warning: variable ‘curNode’ set but not used [-Wunused-but-set-variable] 430 | Agnode_t *head, *tail, *curNode; | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c Rgraphviz.c -o Rgraphviz.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c RgraphvizInit.c -o RgraphvizInit.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c agopen.c -o agopen.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c agread.c -o agread.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c agwrite.c -o agwrite.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c bezier.c -o bezier.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c buildEdgeList.c -o buildEdgeList.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c buildNodeList.c -o buildNodeList.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c doLayout.c -o doLayout.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c graphvizVersion.c -o graphvizVersion.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -Wall -c init.c -o init.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rgraphviz/00new/Rgraphviz/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rgraphviz)
Rgraphviz.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("Rgraphviz") || stop("unable to load Rgraphviz") Loading required package: Rgraphviz Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: grid [1] TRUE > BiocGenerics:::testPackage("Rgraphviz") plotting different layout types dot .... done circo .... done fdp .... done neato .... done osage .... done twopi .... done using toFile with various device types canon . done cmap . done cmapx . done cmapx_np . done dot . done eps . done fig . done gv . done imap . done imap_np . done ismap . done plain . done plain-ext . done ps . done ps2 . done svg . done tk . done vml . done xdot . done RUNIT TEST PROTOCOL -- Wed Nov 20 08:24:21 2024 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : Rgraphviz RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.825 0.095 1.062
Rgraphviz.Rcheck/Rgraphviz-Ex.timings
name | user | system | elapsed | |
AgEdge-class | 0.041 | 0.014 | 0.054 | |
AgNode-class | 0.004 | 0.000 | 0.004 | |
AgTextLabel-class | 0.006 | 0.000 | 0.006 | |
BezierCurve-class | 0.003 | 0.000 | 0.004 | |
GraphvizLayouts | 0.001 | 0.000 | 0.002 | |
Ragraph-class | 0.014 | 0.000 | 0.014 | |
agopen | 0.006 | 0.000 | 0.006 | |
agopenSimple | 0.037 | 0.000 | 0.036 | |
agwrite | 0.004 | 0.000 | 0.004 | |
boundingBox-class | 0.002 | 0.001 | 0.004 | |
buildNodeList | 0.002 | 0.000 | 0.002 | |
clusterData-methods | 0.131 | 0.002 | 0.181 | |
getDefaultAttrs | 0.001 | 0.000 | 0.000 | |
graphLayout | 0.003 | 0.000 | 0.003 | |
graphvizCapabilities | 0.000 | 0.001 | 0.000 | |
graphvizVersion | 0 | 0 | 0 | |
layoutGraph | 0.115 | 0.001 | 0.117 | |
makeNodeAttrs | 0.001 | 0.000 | 0.002 | |
pEdge-class | 0.002 | 0.000 | 0.003 | |
pNode-class | 0.001 | 0.001 | 0.002 | |
pieGlyph | 0.006 | 0.000 | 0.007 | |
plot-methods | 0 | 0 | 0 | |
removedEdges | 0.002 | 0.000 | 0.002 | |
renderGraph | 0.043 | 0.001 | 0.044 | |
toDot-methods | 0.005 | 0.000 | 0.004 | |
toFile | 0.017 | 0.000 | 0.017 | |
xyPoint-class | 0.001 | 0.000 | 0.000 | |