############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Rgraphviz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘Rgraphviz’ ... ** using staged installation configure: Using bundled Graphviz. configure: Searching for the compilers specified by R. checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc accepts -g... yes checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to enable C11 features... none needed checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -E checking whether the compiler supports GNU C++... yes checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 accepts -g... yes checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... 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(cached) yes checking whether the /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking which extension is used for runtime loadable modules... .so checking which variable specifies run-time module search path... LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/NetworkManager/1.44.2-3.oe2403 /usr/lib64/acl /usr/lib64 /usr/lib64/graphviz /usr/lib64 /usr/lib64/libproxy /usr/lib64 /usr/lib64/man-db /usr/lib64/mysql /usr/lib64/openmpi/lib /usr/lib64/pulseaudio/modules /usr/lib64/pulseaudio/ /usr/libexec/sudo /usr/lib64/systemd /usr/lib64/tracker-3.0 /usr/lib64/vala-0.56 /usr/lib64/perl5/CORE checking for library containing dlopen... none required checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for ltdl.h... no checking where to find libltdl headers... -I${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... yes checking for strlcpy... yes checking for X... disabled configure: WARNING: X11 not available. checking tcl.h usability... yes checking tcl.h presence... yes checking for tcl.h... yes configure: WARNING: Unable to find tclConfig.sh. The Tcl packages will not be built configure: WARNING: No Tcl. The Tk packages will not be built either 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... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes 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-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix' 'CC=/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc' 'CXX=/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17' 'CFLAGS=-g -O2 -Wall -Werror=format-security' 'CXXFLAGS=-g -O2 -Wall -Werror=format-security' 'LDFLAGS=-L/usr/local/lib' '--libdir=/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' '--includedir=/home/biocbuild/bbs-3.21-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-4.5.0-devel_2024-11-24/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... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc object... ok checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc static flag -static works... yes checking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc supports -c -o file.o... yes checking if /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc supports -c -o file.o... 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LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/NetworkManager/1.44.2-3.oe2403 /usr/lib64/acl /usr/lib64 /usr/lib64/graphviz /usr/lib64 /usr/lib64/libproxy /usr/lib64 /usr/lib64/man-db /usr/lib64/mysql /usr/lib64/openmpi/lib /usr/lib64/pulseaudio/modules /usr/lib64/pulseaudio/ /usr/libexec/sudo /usr/lib64/systemd /usr/lib64/tracker-3.0 /usr/lib64/vala-0.56 /usr/lib64/perl5/CORE checking for library containing dlopen... none required checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for unistd.h... (cached) yes checking for dl.h... no checking for sys/dl.h... no checking for dld.h... no checking for mach-o/dyld.h... no checking for dirent.h... yes checking for closedir... yes checking for opendir... yes checking for readdir... yes checking for strlcat... yes checking for strlcpy... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands ---------------------------------------------------------------- graphviz-2.28.0 will be compiled with the following: options: cgraph: No (disabled by default - experimental) digcola: Yes expat: No (disabled) fontconfig: No (disabled) freetype: No (disabled) glut: No (disabled) gts: No (disabled) ipsepcola: No (disabled by default - C++ portability issues) ltdl: No (disabled) ortho: Yes png: No (disabled) jpeg: No (disabled) sfdp: Yes shared: No (disabled) static: Yes qt: No (qmake not found) commands: dot: Yes (always enabled) neato: Yes (always enabled) fdp: Yes (always enabled) circo: Yes (always enabled) twopi: Yes (always enabled) gvpr: Yes (always enabled) gvmap: Yes (always enabled) lefty: 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 (tcl not available) tcldot: No (tcl not available) tclpathplan: No (tcl not available) gdtclft: No (tcl 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-3.21-bioc/meat/Rgraphviz/src/graphviz' Making install in libltdl make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl' make install-am make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl' /bin/sh ./libtool --tag=CC --mode=compile /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c libtool: compile: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -g -O2 -Wall -Werror=format-security -module -avoid-version -L/usr/local/lib -o dlopen.la dlopen.lo 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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -Werror=format-security -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=link /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -g -O2 -Wall -Werror=format-security -no-undefined -dlpreopen dlopen.la -L/usr/local/lib -o libltdlc.la libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT libtool: link: (cd .libs && /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -g -O2 -Wall -Werror=format-security -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-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a") libtool: link: ar cru .libs/libltdlc.a libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o .libs/libltdlcS.o .libs/libltdlc.lax/dlopen.a/dlopen.o 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-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl' Making install in lib make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib' Making install in cdt make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libcdt.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libcdt.lai /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.la libtool: install: /usr/bin/install -c .libs/libcdt.a /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libcdt.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 cdt.3 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 cdt.3.pdf '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libcdt.pc '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 cdt.h '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/cdt' Making install in graph make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/graph' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libgraph.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libgraph.lai /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.la libtool: install: /usr/bin/install -c .libs/libgraph.a /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgraph.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 graph.3 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 graph.3.pdf '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgraph.pc '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graph.h '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/graph' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/graph' Making install in pathplan make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libpathplan.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libpathplan.lai /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.la libtool: install: /usr/bin/install -c .libs/libpathplan.a /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libpathplan.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pathplan.3 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pathplan.3.pdf '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libpathplan.pc '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/pathplan' Making install in vpsc make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' make[4]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/vpsc' Making install in rbtree make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/rbtree' Making install in ortho make[3]: Entering directory '/home/biocbuild/bbs-3.21-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 /usr/include/bits/libc-header-start.h:33, from /usr/include/string.h:26, from trapezoid.c:19: /usr/include/features.h:347:10: note: this is the location of the previous definition 347 | # define __USE_ISOC99 1 | ^~~~~~~~~~~~ trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] 66 | static int newnode() | ^~~~~~~ trapezoid.c: In function 'add_segment': trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable] 437 | int tritop = 0, tribot = 0, is_swapped; | ^~~~~~ trapezoid.c: In function 'add_segment.isra': trapezoid.c:996:3: warning: 'tfirstr' may be used uninitialized [-Wmaybe-uninitialized] 996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ trapezoid.c:434:7: note: 'tfirstr' was declared here 434 | int tfirstr, tlastr, tfirstl, tlastl; | ^~~~~~~ trapezoid.c:996:3: warning: 'tlastr' may be used uninitialized [-Wmaybe-uninitialized] 996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ trapezoid.c:434:16: note: 'tlastr' was declared here 434 | int tfirstr, tlastr, tfirstl, tlastl; | ^~~~~~ CCLD libortho_C.la make[4]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/ortho' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/ortho' Making install in sparse make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' CC SparseMatrix.lo SparseMatrix.c: In function 'SparseMatrix_import_binary': SparseMatrix.c:629:48: warning: variable 'iread' set but not used [-Wunused-but-set-variable] 629 | int m, n, nz, nzmax, type, format, property, iread; | ^~~~~ CC general.lo CC BinaryHeap.lo In file included from general.h:21, from BinaryHeap.h:17, from BinaryHeap.c:14: BinaryHeap.c: In function 'BinaryHeap_sanity_check': BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 269 | for (i = 0; i < h->len + IntStack_get_length(h->id_stack); i++) assert(mask[i] =- 1); | ^~~~ CC IntStack.lo CCLD libsparse_C.la make[4]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/sparse' Making install in patchwork make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/patchwork' Making install in common make[3]: Entering directory '/home/biocbuild/bbs-3.21-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 render.h:47, from ../../lib/common/htmlparse.y:16: ../../lib/common/htmlparse.y: In function 'appendFItemList': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:193:25: note: in expansion of macro 'agxbuse' 193 | fi->ti.str = strdup(agxbuse(ag)); | ^~~~~~~ ../../lib/common/htmlparse.y: In function 'htmlparse': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:500:24: note: in expansion of macro 'agxbuse' 500 | if (nonSpace(agxbuse(HTMLstate.str))) { | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:511:24: note: in expansion of macro 'agxbuse' 511 | if (nonSpace(agxbuse(HTMLstate.str))) { | ^~~~~~~ CC htmltable.lo In file included from render.h:47, from htmltable.c:35: htmltable.c: In function 'initAnchor': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmltable.c:299:14: note: in expansion of macro 'agxbuse' 299 | id = agxbuse (&xb); | ^~~~~~~ htmltable.c: In function 'nameOf': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmltable.c:1665:12: note: in expansion of macro 'agxbuse' 1665 | return agxbuse(xb); | ^~~~~~~ htmltable.c: In function 'make_html_label': htmltable.c:1828:12: warning: 'env.g' may be used uninitialized [-Wmaybe-uninitialized] 1828 | g = env.g->root; | ~~~^~ htmltable.c:1809:15: note: 'env' declared here 1809 | htmlenv_t env; | ^~~ CC input.lo input.c: In function 'dotneato_basename': input.c:136:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 136 | while (*s) s++; s--; | ^~~~~ input.c:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 136 | while (*s) s++; s--; | ^ In file included from render.h:47, from input.c:15: input.c: In function 'global_def': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ input.c:200:24: note: in expansion of macro 'agxbuse' 200 | sym = dclfun(NULL, agxbuse (xb), rhs); | ^~~~~~~ CC pointset.lo CC postproc.lo CC routespl.lo CC splines.lo CC psusershape.lo psusershape.c: In function 'user_init': psusershape.c:49:30: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int saw_bb, must_inline, rc; | ^~ In file included from render.h:47, from psusershape.c:20: psusershape.c: In function 'ps_string': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ psusershape.c:303:5: note: in expansion of macro 'agxbputc' 303 | agxbputc (&xb, RPAREN); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ psusershape.c:305:9: note: in expansion of macro 'agxbuse' 305 | s = agxbuse(&xb); | ^~~~~~~ psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 268 | int rc; | ^~ CC timing.lo CC labels.lo labels.c: In function 'xml_url_string': labels.c:561:21: warning: variable 'prev' set but not used [-Wunused-but-set-variable] 561 | char *p, *sub, *prev = NULL; | ^~~~ CC ns.lo CC shapes.lo CC utils.lo utils.c: In function 'chkPort': utils.c:690:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 690 | else | ^~~~ utils.c:692:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 692 | pt.name = s; | ^~ In file included from render.h:47, from utils.c:14: utils.c: In function 'clustNode': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:950:5: note: in expansion of macro 'agxbputc' 950 | agxbputc(xb, ':'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:954:29: note: in expansion of macro 'agxbuse' 954 | cn = agnode(agroot(cg), agxbuse(xb)); | ^~~~~~~ utils.c: In function 'scanEntity': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1359:5: note: in expansion of macro 'agxbputc' 1359 | agxbputc(xb, '&'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1369:5: note: in expansion of macro 'agxbputc' 1369 | agxbputc(xb, '#'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1371:5: note: in expansion of macro 'agxbputc' 1371 | agxbputc(xb, ';'); | ^~~~~~~~ utils.c: In function 'htmlEntityUTF8': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1515:18: note: in expansion of macro 'agxbuse' 1515 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1456:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1456 | int rc; | ^~ utils.c: In function 'latin1ToUTF8': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1555:18: note: in expansion of macro 'agxbuse' 1555 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1531:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1531 | int rc; | ^~ utils.c: In function 'utf8ToLatin1': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1587:18: note: in expansion of macro 'agxbuse' 1587 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1573:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1573 | int rc; | ^~ CC geom.lo CC output.lo In file included from render.h:47, from output.c:14: output.c: In function 'attach_attrs_and_arrows': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:350:29: note: in expansion of macro 'agxbuse' 350 | agset(n, "pos", agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:373:31: note: in expansion of macro 'agxbuse' 373 | agset(n, "rects", agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:391:25: note: in expansion of macro 'agxbputc' 391 | agxbputc(&xb, ' '); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:403:46: note: in expansion of macro 'agxbuse' 403 | agxset(n, N_vertices->index, agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:417:25: note: in expansion of macro 'agxbputc' 417 | agxbputc(&xb, ';'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:434:29: note: in expansion of macro 'agxbputc' 434 | agxbputc(&xb, ' '); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:440:33: note: in expansion of macro 'agxbuse' 440 | agset(e, "pos", agxbuse(&xb)); | ^~~~~~~ CC emit.lo In file included from render.h:47, from emit.c:25: emit.c: In function 'getObjId': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:212:9: note: in expansion of macro 'agxbputc' 212 | agxbputc (xb, '_'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:218:12: note: in expansion of macro 'agxbuse' 218 | return agxbuse(xb); | ^~~~~~~ emit.c: In function 'emit_xdot': emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable] 941 | char* fontname; | ^~~~~~~~ emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable] 940 | double fontsize; | ^~~~~~~~ emit.c: In function 'selectedlayer': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:1152:22: note: in expansion of macro 'agxbuse' 1152 | w1 = w0 = strtok(agxbuse(&xb), gvc->layerDelims); | ^~~~~~~ emit.c: In function 'nodeIntersect': emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable] 2247 | char* target; | ^~~~~~ emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable] 2246 | char* tooltip; | ^~~~~~~ emit.c: In function 'xdotBB': emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable] 2474 | pointf sz; | ^~ emit.c: In function 'style_token': emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 3262 | int token, rc; | ^~ emit.c: In function 'parse_style': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:3356:17: note: in expansion of macro 'agxbputc' 3356 | agxbputc(&ps_xb, '\0'); /* terminate previous */ | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:3359:29: note: in expansion of macro 'agxbuse' 3359 | agxbput(&ps_xb, agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:3360:13: note: in expansion of macro 'agxbputc' 3360 | agxbputc(&ps_xb, '\0'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:3372:11: note: in expansion of macro 'agxbuse' 3372 | (void)agxbuse(&ps_xb); /* adds final '\0' to buffer */ | ^~~~~~~ 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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/common' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/common' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/common' Making install in pack make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/pack' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pack.3 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pack.3.pdf '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pack.h '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/pack' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/pack' Making install in xdot make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' CC xdot.lo xdot.c: In function 'sprintXDot': xdot.c:537:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 537 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xdot.c:538:21: note: in expansion of macro 'agxbputc' 538 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ xdot.c:606:16: note: in expansion of macro 'agxbuse' 606 | s = strdup(agxbuse(&xb)); | ^~~~~~~ CCLD libxdot.la CCLD libxdot_C.la make[4]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libxdot.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libxdot.lai /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.la libtool: install: /usr/bin/install -c .libs/libxdot.a /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libxdot.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 xdot.3 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 xdot.3.pdf '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libxdot.pc '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 xdot.h '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/xdot' Making install in gvc make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' CC gvrender.lo CC gvlayout.lo CC gvdevice.lo In file included from ../../lib/common/types.h:18, from gvplugin_device.h:17, from gvdevice.c:55: gvdevice.c: In function 'gvfwrite': gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 269 | assert(size = sizeof(char)); | ^~~~ CC gvloadimage.lo CC gvcontext.lo CC gvjobs.lo CC gvevent.lo CC gvplugin.lo In file included from gvplugin.c:23: gvplugin.c: In function 'gvplugin_list': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:392:17: note: in expansion of macro 'agxbputc' 392 | agxbputc(&xb,' '); agxbput(&xb, (*pnext)->typestr); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:393:17: note: in expansion of macro 'agxbputc' 393 | agxbputc(&xb,':'); agxbput(&xb, (*pnext)->package->name); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:410:17: note: in expansion of macro 'agxbputc' 410 | agxbputc(&xb,' '); agxbput(&xb, q); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvplugin.c:423:14: note: in expansion of macro 'agxbuse' 423 | bp = agxbuse(&xb); | ^~~~~~~ CC gvconfig.lo CC gvtextlayout.lo CC gvusershape.lo gvusershape.c: In function 'gvusershape_open': gvusershape.c:415:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 415 | if (!(us->data = (void*)find_user_shape(us->name))) | ^~ gvusershape.c:417:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 417 | free(us); | ^~~~ CC gvc.lo CCLD libgvc.la CCLD libgvc_C.la make[4]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' /bin/sh ../../libtool --mode=install /usr/bin/install -c libgvc.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libgvc.lai /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.la libtool: install: /usr/bin/install -c .libs/libgvc.a /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/libgvc.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 gvc.3 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man3' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 gvc.3.pdf '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgvc.pc '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/gvc' Making install in circogen make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/circogen' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/circogen' Making install in dotgen make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/dotgen' Making install in fdpgen make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/fdpgen' Making install in neatogen make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/neatogen' Making install in twopigen make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/twopigen' Making install in sfdpgen make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/sfdpgen' Making install in osage make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/osage' CC osageinit.lo CCLD libosage_C.la make[4]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/osage' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib/osage' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib' make[4]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/lib' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/lib' Making install in plugin make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin' Making install in core make[3]: Entering directory '/home/biocbuild/bbs-3.21-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 # for read() declaration | ^ CCLD libgvplugin_core_C.la CCLD libgvplugin_core.la make[4]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/core' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_core.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/core' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/core' Making install in dot_layout make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_dot_layout.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/dot_layout' Making install in neato_layout make[3]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' /bin/sh ../../libtool --mode=install /usr/bin/install -c libgvplugin_neato_layout.la '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/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-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin/neato_layout' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin' make[4]: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/plugin' make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man7' /usr/bin/install -c -m 644 graphviz.7 '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/man/man7' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graphviz_version.h '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/include/graphviz' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc' /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/share/graphviz/doc' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz' make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz' cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix/lib/graphviz' cp: -r not specified; omitting directory '/home/biocbuild/bbs-3.21-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-3.21-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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -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; | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c Rgraphviz.c -o Rgraphviz.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c RgraphvizInit.c -o RgraphvizInit.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c agopen.c -o agopen.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c agread.c -o agread.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c agwrite.c -o agwrite.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c bezier.c -o bezier.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c buildEdgeList.c -o buildEdgeList.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c buildNodeList.c -o buildNodeList.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c doLayout.c -o doLayout.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c graphvizVersion.c -o graphvizVersion.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.21-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 -Werror=format-security -c init.c -o init.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)