| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:08 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Rgraphviz |
| Version: 2.50.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL Rgraphviz |
| StartedAt: 2024-11-19 20:30:00 -0000 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 20:32:02 -0000 (Tue, 19 Nov 2024) |
| EllapsedTime: 122.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL Rgraphviz
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/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... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-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... 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 library containing strerror... none required
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... none needed
checking whether yytext is a pointer... no
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... /home/biocbuild/miniforge3/bin/tclsh8.6
checking whether gcc and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking dependency style of g++ -std=gnu++17... gcc3
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... 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 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 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
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checking stdarg.h usability... yes
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checking sys/ioctl.h usability... yes
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checking whether time.h and sys/time.h may both be included... yes
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checking for library containing opendir... none required
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checking for fgrep... grep -F
checking for ld used by gcc... /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld
checking if the linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/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 /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/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 we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
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 (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) 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... no
checking for dlopen in -ldl... 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... /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld
checking if the linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) is GNU ld... yes
checking whether the g++ -std=gnu++17 linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) 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 (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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/lib64/NetworkManager/1.32.12-20.oe2203sp1 /usr/lib64/acl /usr/lib64 /usr/lib64 /usr/lib64/graphviz /usr/lib64 /usr/lib64 /usr/lib64 /usr/lib64 /usr/lib64/man-db /usr/lib64/mysql /usr/lib64/openmpi/lib /usr/lib64/pulse-15.0/modules /usr/lib64/pulseaudio/ /usr/libexec/sudo /usr/lib/systemd /home/abuild/rpmbuild/BUILD/texlive-20180414-source/source/inst/lib /usr/lib64/tracker-3.0 /usr/lib64/perl5/CORE
checking for library containing dlopen... -ldl
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
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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... no
checking where to find libltdl headers... -I${top_srcdir}/libltdl
checking where to find libltdl library... ${top_build_prefix}libltdl/libltdlc.la
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... no
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checking for X... disabled
configure: WARNING: X11 not available.
using tcl headers from -I/home/biocbuild/miniforge3/include
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
using /home/biocbuild/miniforge3/lib/tclConfig.sh
checking for wish8.6... /home/biocbuild/miniforge3/bin/wish8.6
using tk headers from -I/home/biocbuild/miniforge3/include
checking tk.h usability... no
checking tk.h presence... no
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configure: WARNING: Unable to find header tk.h. The Tk packages will not be built
checking for tk.h... (cached) no
checking tkInt.h usability... no
checking tkInt.h presence... no
checking for tkInt.h... no
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking X11/Intrinsic.h usability... no
checking X11/Intrinsic.h presence... no
checking for X11/Intrinsic.h... no
checking for X11/Xaw/Text.h... no
configure: WARNING: Optional Xaw library not available - missing headers
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking for deflateBound... yes
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... no
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 (/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/home/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=/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/home/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=/home/biocbuild/R/R-4.4.1/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/R/R/site-library' '--enable-ltdl-convenience' --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... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-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... /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld
checking if the linker (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/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 /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/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 (/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/bin/ld) 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... no
checking for dlopen in -ldl... 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/lib64/NetworkManager/1.32.12-20.oe2203sp1 /usr/lib64/acl /usr/lib64 /usr/lib64 /usr/lib64/graphviz /usr/lib64 /usr/lib64 /usr/lib64 /usr/lib64 /usr/lib64/man-db /usr/lib64/mysql /usr/lib64/openmpi/lib /usr/lib64/pulse-15.0/modules /usr/lib64/pulseaudio/ /usr/libexec/sudo /usr/lib/systemd /home/abuild/rpmbuild/BUILD/texlive-20180414-source/source/inst/lib /usr/lib64/tracker-3.0 /usr/lib64/perl5/CORE
checking for library containing dlopen... -ldl
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... no
checking for strlcpy... no
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: No (missing Xaw headers)
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: No (tk not available)
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make install-recursive
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make install-am
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl'
/bin/sh ./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/sh ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -module -avoid-version -L/usr/local/lib -o dlopen.la dlopen.lo -ldl -ldl
libtool: link: ar cru .libs/dlopen.a dlopen.o
libtool: link: ranlib .libs/dlopen.a
libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )
/bin/sh ./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/sh ./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/sh ./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/sh ./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/sh ./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/sh ./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/sh ./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 lt__strl.lo -MD -MP -MF .deps/lt__strl.Tpo -c -o lt__strl.lo lt__strl.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 lt__strl.lo -MD -MP -MF .deps/lt__strl.Tpo -c lt__strl.c -fPIC -DPIC -o lt__strl.o
mv -f .deps/lt__strl.Tpo .deps/lt__strl.Plo
/bin/sh ./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 lt__strl.lo -ldl
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 "/home/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 lt__strl.o .libs/libltdlcS.o .libs/libltdlc.lax/dlopen.a/dlopen.o
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" )
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl'
make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/libltdl'
Making install in lib
make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib'
Making install in cdt
make[3]: Entering directory '/home/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
CCLD libcdt_C.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libcdt.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libcdt.lai /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.la
libtool: install: /usr/bin/install -c .libs/libcdt.a /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 cdt.3 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 cdt.3.pdf '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libcdt.pc '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 cdt.h '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/cdt'
Making install in graph
make[3]: Entering directory '/home/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
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)
| ~~~~~~~~~~~~~~~^~~~~
CC node.lo
CC parser.lo
CC refstr.lo
CC trie.lo
CCLD libgraph.la
CCLD libgraph_C.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgraph.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgraph.lai /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.la
libtool: install: /usr/bin/install -c .libs/libgraph.a /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 graph.3 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 graph.3.pdf '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libgraph.pc '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 graph.h '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/graph'
Making install in pathplan
make[3]: Entering directory '/home/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
CCLD libpathplan_C.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libpathplan.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libpathplan.lai /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.la
libtool: install: /usr/bin/install -c .libs/libpathplan.a /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 pathplan.3 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 pathplan.3.pdf '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libpathplan.pc '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 pathgeom.h pathplan.h '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan'
Making install in vpsc
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc'
Making install in rbtree
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree'
Making install in ortho
make[3]: Entering directory '/home/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;
| ^~
ortho.c: In function 'putSeg':
ortho.c:545:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
545 | fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->p.p1,seg->comm_coord,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
546 | seg->p.p2, seg->comm_coord, bendToStr (seg->l1), bendToStr (seg->l2));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
ortho.c:545:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
545 | fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->p.p1,seg->comm_coord,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
546 | seg->p.p2, seg->comm_coord, bendToStr (seg->l1), bendToStr (seg->l2));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
ortho.c:542:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
542 | fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->comm_coord, seg->p.p1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
543 | seg->comm_coord, seg->p.p2, bendToStr (seg->l1), bendToStr (seg->l2));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
ortho.c:542:5: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
542 | fprintf (fp, "((%f,%f),(%f,%f)) %s %s", seg->comm_coord, seg->p.p1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
543 | seg->comm_coord, seg->p.p2, bendToStr (seg->l1), bendToStr (seg->l2));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:212:7: warning: 'tp' may be used uninitialized [-Wmaybe-uninitialized]
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:22:9: warning: "__USE_ISOC99" redefined
22 | #define __USE_ISOC99
| ^~~~~~~~~~~~
In file included from /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/string.h:25,
from trapezoid.c:19:
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/features.h:257:10: note: this is the location of the previous definition
257 | # 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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/ortho'
Making install in sparse
make[3]: Entering directory '/home/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
CC IntStack.lo
CCLD libsparse_C.la
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sparse'
Making install in patchwork
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork'
Making install in common
make[3]: Entering directory '/home/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;
| ^~~~
CC colxlate.lo
CC fontmetrics.lo
CC args.lo
CC memory.lo
CC globals.lo
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));
| ^~~~~~~
CC htmlparse.lo
In file included from /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/string.h:633,
from render.h:37,
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/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/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/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/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/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/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));
| ^~~~~~~
In file included from render.h:47:
../../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, ';');
| ^~~~~~~~
In file included from /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/string.h:633,
from render.h:37:
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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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));
| ^~~~~~~
../../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 */
| ^~~~~~~
emit.c: In function 'getObjId':
emit.c:215:5: warning: 'idnum' may be used uninitialized [-Wmaybe-uninitialized]
215 | sprintf (buf, "%ld", idnum);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
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: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: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: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;
| ^~
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:1932:58: 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;
| ^~
CCLD libcommon_C.la
make[4]: Entering directory '/home/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 '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/common'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/common'
Making install in pack
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 pack.3 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 pack.3.pdf '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 pack.h '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pack'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/pack'
Making install in xdot
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
CC xdot.lo
In file included from /home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/string.h:633,
from xdot.c:16:
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));
| ^~~~~~~
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));
| ^~~~~~~
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));
| ^~~~~~~
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));
| ^~~~~~~
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));
| ^~~~~~~
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));
| ^~~~~~~
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
CCLD libxdot_C.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libxdot.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libxdot.lai /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.la
libtool: install: /usr/bin/install -c .libs/libxdot.a /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 xdot.3 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 xdot.3.pdf '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libxdot.pc '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 xdot.h '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/xdot'
Making install in gvc
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
CC gvrender.lo
CC gvlayout.lo
CC gvdevice.lo
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
CCLD libgvc_C.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvc.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib'
libtool: install: /usr/bin/install -c .libs/libgvc.lai /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.la
libtool: install: /usr/bin/install -c .libs/libgvc.a /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/install -c -m 644 gvc.3 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man3'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/install -c -m 644 gvc.3.pdf '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/install -c -m 644 libgvc.pc '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig'
/usr/bin/mkdir -p '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
make[4]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/gvc'
Making install in circogen
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/circogen'
Making install in dotgen
make[3]: Entering directory '/home/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;
| ^~
In function 'makeSimpleFlatLabels',
inlined from 'make_flat_adj_edges' at dotsplines.c:1117:6,
inlined from 'make_flat_edge' at dotsplines.c:1457:2,
inlined from '_dot_splines' at dotsplines.c:440:6:
dotsplines.c:997:25: warning: 'lminx' may be used uninitialized [-Wmaybe-uninitialized]
997 | points[7].x = lminx;
| ~~~~~~~~~~~~^~~~~~~
dotsplines.c: In function '_dot_splines':
dotsplines.c:882:12: note: 'lminx' was declared here
882 | double lminx, lmaxx;
| ^~~~~
In function 'makeSimpleFlatLabels',
inlined from 'make_flat_adj_edges' at dotsplines.c:1117:6,
inlined from 'make_flat_edge' at dotsplines.c:1457:2,
inlined from '_dot_splines' at dotsplines.c:440:6:
dotsplines.c:993:25: warning: 'lmaxx' may be used uninitialized [-Wmaybe-uninitialized]
993 | points[5].x = lmaxx;
| ~~~~~~~~~~~~^~~~~~~
dotsplines.c: In function '_dot_splines':
dotsplines.c:882:19: note: 'lmaxx' was declared here
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:736:25: warning: 'maxLayerIndex' may be used uninitialized [-Wmaybe-uninitialized]
736 | qsort(layerWidthInfo[maxLayerIndex].nodeGroupsInLayer,
| ^
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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen'
Making install in fdpgen
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen'
Making install in neatogen
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen'
Making install in twopigen
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen'
Making install in sfdpgen
make[3]: Entering directory '/home/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
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen'
Making install in osage
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
CC osageinit.lo
CCLD libosage_C.la
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib/osage'
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib'
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib'
make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/lib'
Making install in plugin
make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin'
Making install in core
make[3]: Entering directory '/home/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
CCLD libgvplugin_core.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_core.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la
libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/core'
Making install in dot_layout
make[3]: Entering directory '/home/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
CCLD libgvplugin_dot_layout.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_dot_layout.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /home/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 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout'
Making install in neato_layout
make[3]: Entering directory '/home/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
CCLD libgvplugin_neato_layout.la
make[4]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_neato_layout.la '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /home/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 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: install: ranlib /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a
libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/miniforge3/bin:/home/biocbuild/miniforge3/condabin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz
----------------------------------------------------------------------
Libraries have been installed in:
/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout'
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[4]: Entering directory '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz/plugin'
make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz'
make[3]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
/usr/bin/install -c -m 644 graphviz.7 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/man/man7'
/usr/bin/mkdir -p '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/install -c -m 644 graphviz_version.h '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/include/graphviz'
/usr/bin/mkdir -p '/home/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 '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc'
make[3]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz'
make[2]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz'
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/graphviz'
cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.20-bioc/meat/Rgraphviz/src/libunix/lib/graphviz'
cp: -r not specified; omitting directory '/home/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/home/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 (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -I/home/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/R/R-4.4.1/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/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)