Kasper Daniel Hansen
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/Rgraphviz |
| git_branch: devel |
| git_last_commit: 86e5661 |
| git_last_commit_date: 2024-10-29 09:21:30 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:15 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1723/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rgraphviz 2.51.0 (landing page) Kasper Daniel Hansen
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the Rgraphviz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rgraphviz.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Rgraphviz |
| Version: 2.51.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Rgraphviz_2.51.0.tar.gz |
| StartedAt: 2024-11-28 05:04:51 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 05:09:13 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 262.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rgraphviz.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Rgraphviz.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Rgraphviz_2.51.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK
* this is package ‘Rgraphviz’ version ‘2.51.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rgraphviz’ can be installed ... WARNING
Found the following significant warnings:
WARNING: `aclocal-1.12' is missing on your system. You should only need it if
WARNING: `automake-1.12' is missing on your system. You should only need it if
./ltdl.h:44:27: warning: the address of 'libext' will always evaluate as 'true' [-Waddress]
dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign]
lexer.c:435:33: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign]
lexer.c:435:41: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign]
lexer.c:527:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
route.c:107:29: warning: argument 4 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=]
shortest.c:103:47: warning: argument 2 of type 'Ppoint_t *' {aka 'struct Pxy_t *'} declared as a pointer [-Warray-parameter=]
trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
patchwork.c:231:12: warning: pointer 'cp' used after 'free' [-Wuse-after-free]
gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.graphviz_build_version’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/Rgraphviz/libs/Rgraphviz.so’:
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘srand’, possibly from ‘srand’ (C)
Found ‘srand48’, possibly from ‘srand48’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz.Rcheck/00check.log’
for details.
Rgraphviz.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rgraphviz
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Rgraphviz’ ...
** using staged installation
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
configure: Preparing to compile Graphviz.
configure: Configuring bundled Graphviz.
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for sed... /usr/bin/sed
checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... /usr/bin/tclsh8.6
checking whether gcc and cc understand -c and -o together... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking dependency style of g++ -std=gnu++17... gcc3
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
checking dependency style of gcc... gcc3
checking for inline... inline
checking for windres... no
checking for an ANSI C-conforming const... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... grep
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uid_t in sys/types.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stddef.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for stdint.h... (cached) yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking search.h usability... yes
checking search.h presence... yes
checking for search.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking for sys/types.h... (cached) yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking sys/fpu.h usability... no
checking sys/fpu.h presence... no
checking for sys/fpu.h... no
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/inotify.h usability... yes
checking sys/inotify.h presence... yes
checking for sys/inotify.h... yes
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for socklen_t... yes
checking for bool... yes
checking for struct dioattr... no
checking for main in -lm... yes
checking for feenableexcept... yes
checking for fesetenv... yes
checking libgen.h usability... yes
checking libgen.h presence... yes
checking for libgen.h... yes
checking for basename in -lgen... no
checking for working alloca.h... yes
checking for alloca... yes
checking for lrand48... yes
checking for drand48... yes
checking for srand48... yes
checking for setmode... no
checking for setenv... yes
checking for getenv... yes
checking for __freadable... yes
checking for _sysconf... no
checking for getrusage... yes
checking for strerror... yes
checking for cbrt... no
checking for lsqrt... no
checking for vsnprintf... yes
checking for strtoul... yes
checking for strtoll... yes
checking for strtoull... yes
checking for uname... yes
checking for memset... yes
checking for nl_langinfo... yes
checking for pow... no
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... (cached) yes
checking for strstr... yes
checking for _NSGetEnviron... no
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for strcasestr... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking dependency style of g++ -std=gnu++17... (cached) gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ld used by g++ -std=gnu++17... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++17 static flag -static works... yes
checking if g++ -std=gnu++17 supports -c -o file.o... yes
checking if g++ -std=gnu++17 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for ltdl.h... yes
checking whether lt_dlinterface_register is declared... yes
checking for lt_dladvise_preload in -lltdl... yes
checking where to find libltdl headers...
checking where to find libltdl library... -lltdl
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking for X... disabled
configure: WARNING: X11 not available.
using tcl headers from -I/usr/include/tcl8.6 -I/usr/include/tcl8.6/generic
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
using /usr/lib/tclConfig.sh
checking for wish8.6... /usr/bin/wish8.6
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking for tk.h... (cached) yes
checking tkInt.h usability... no
checking tkInt.h presence... no
checking for tkInt.h... no
using /usr/lib/tkConfig.sh
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... 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... no
checking for GDK_PIXBUF... yes
checking for GTK... yes
checking for GTKGL... no
checking for GTKGLEXT... no
checking for GLADE... no
checking for qmake-qt4... no
checking for qmake-qt3... no
checking for qmake... no
checking for sincos... yes
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... yes
checking if errno externs are declared... no
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix' 'CC=gcc' 'CXX=g++ -std=gnu++17' 'CFLAGS=-g -O2 -Wall' 'CXXFLAGS=-g -O2 -Wall' 'LDFLAGS=-L/usr/local/lib' '--libdir=/home/biocbuild/bbs-3.21-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/bbs-3.21-bioc/R/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/bbs-3.21-bioc/R/site-library' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
----------------------------------------------------------------
graphviz-2.28.0 will be compiled with the following:
options:
cgraph: No (disabled by default - experimental)
digcola: Yes
expat: No (disabled)
fontconfig: No (disabled)
freetype: No (disabled)
glut: No (disabled)
gts: No (disabled)
ipsepcola: No (disabled by default - C++ portability issues)
ltdl: No (disabled)
ortho: Yes
png: No (disabled)
jpeg: No (disabled)
sfdp: Yes
shared: No (disabled)
static: Yes
qt: No (qmake not found)
commands:
dot: Yes (always enabled)
neato: Yes (always enabled)
fdp: Yes (always enabled)
circo: Yes (always enabled)
twopi: Yes (always enabled)
gvpr: Yes (always enabled)
gvmap: Yes (always enabled)
lefty: No (missing Xaw headers)
smyrna: No (disabled by default - experimental)
gvedit: No (qmake not found)
plugin libraries:
dot_layout: Yes (always enabled)
neato_layout: Yes (always enabled)
core: Yes (always enabled)
devil: No (disabled)
gd: No (disabled)
gdiplus: No (disabled by default - Windows only)
gdk_pixbuf: Yes
ghostscript: No (disabled)
glitz: No (disabled by default - incomplete)
gtk: Yes
lasi: No (disabled)
ming: No (disabled by default - incomplete)
pangocairo: No (disabled)
quartz: No (disabled by default - Mac only)
rsvg: No (disabled)
visio: No (disabled by default - experimental)
xlib: No (disabled or unavailable)
language extensions:
gv_sharp: No (swig not available)
gv_go: No (disabled by default - experimental)
gv_guile: No (swig not available)
gv_io: No (disabled by default - no swig support yet)
gv_java: No (swig not available)
gv_lua: No (swig not available)
gv_ocaml: No (swig not available)
gv_perl: No (swig not available)
gv_php: No (swig not available)
gv_python: No (swig not available)
gv_python23: No (disabled by default - for multiversion installs)
gv_python24: No (disabled by default - for multiversion installs)
gv_python25: No (disabled by default - for multiversion installs)
gv_python26: No (disabled by default - for multiversion installs)
gv_python27: No (disabled by default - for multiversion installs)
gv_R: No (swig not available)
gv_ruby: No (swig not available)
gv_tcl: No (swig not available)
tcldot: Yes
tclpathplan: Yes
gdtclft: No (gd not available)
tkspline: Yes
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/config/missing --run aclocal-1.12 -I m4
/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system. You should only need it if
you modified `acinclude.m4' or `configure.ac'. You might want
to install the `Automake' and `Perl' packages. Grab them from
any GNU archive site.
cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/config/missing --run automake-1.12 --gnu
/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system. You should only need it if
you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
You might want to install the `Automake' and `Perl' packages.
Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoconf
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
configure.ac:185: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:185: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_INIT_AUTOMAKE-invocation
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:599: AM_INIT_AUTOMAKE is expanded from...
configure.ac:185: the top level
configure.ac:252: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete
./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from...
./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from...
aclocal.m4:781: AM_PROG_LEX is expanded from...
configure.ac:252: the top level
configure.ac:374: warning: The macro `AC_HEADER_TIME' is obsolete.
configure.ac:374: You should run autoupdate.
./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
configure.ac:374: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:467: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5343: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
m4/libtool.m4:796: _LT_LANG_DEFAULT_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:467: the top level
configure.ac:2722: warning: The macro `AC_TRY_LINK' is obsolete.
configure.ac:2722: You should run autoupdate.
./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/iconv.m4:22: AM_ICONV_LINK is expanded from...
m4/iconv.m4:77: AM_ICONV is expanded from...
configure.ac:2722: the top level
configure.ac:2722: warning: The macro `AC_TRY_COMPILE' is obsolete.
configure.ac:2722: You should run autoupdate.
./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
m4/iconv.m4:77: AM_ICONV is expanded from...
configure.ac:2722: the top level
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure CC=gcc CXX=g++ -std=gnu++17 CFLAGS=-g -O2 -Wall CXXFLAGS=-g -O2 -Wall LDFLAGS=-L/usr/local/lib --prefix=/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix --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/bbs-3.21-bioc/R/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/bbs-3.21-bioc/R/site-library --no-create --no-recursion
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for sed... /usr/bin/sed
checking for grep... grep
checking for sort... sort
checking for groff... groff
checking for ps2pdf... ps2pdf
checking for pstopdf... (cached) ps2pdf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for tclsh8.6... /usr/bin/tclsh8.6
checking whether gcc and cc understand -c and -o together... yes
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking dependency style of g++ -std=gnu++17... gcc3
checking for gcc... gcc
checking whether the compiler supports GNU Objective C... yes
checking whether gcc accepts -g... yes
checking dependency style of gcc... gcc3
checking for inline... inline
checking for windres... no
checking for an ANSI C-conforming const... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/time.h... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... grep
checking for egrep... grep -E
checking for uid_t in sys/types.h... yes
checking for stdarg.h... yes
checking for stddef.h... yes
checking for stddef.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for stdint.h... (cached) yes
checking for malloc.h... yes
checking for fcntl.h... yes
checking for search.h... yes
checking for getopt.h... yes
checking for pthread.h... yes
checking for values.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for termios.h... yes
checking for errno.h... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for fenv.h... yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for setjmp.h... yes
checking for sys/time.h... (cached) yes
checking for sys/times.h... yes
checking for sys/types.h... (cached) yes
checking for sys/select.h... yes
checking for fpu_control.h... yes
checking for sys/fpu.h... no
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/mman.h... yes
checking for sys/ioctl.h... yes
checking for sys/inotify.h... yes
checking for langinfo.h... yes
checking for libintl.h... yes
checking for crt_externs.h... no
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for socklen_t... yes
checking for bool... yes
checking for struct dioattr... no
checking for main in -lm... yes
checking for feenableexcept... yes
checking for fesetenv... yes
checking for libgen.h... yes
checking for basename in -lgen... no
checking for working alloca.h... yes
checking for alloca... yes
checking for lrand48... yes
checking for drand48... yes
checking for srand48... yes
checking for setmode... no
checking for setenv... yes
checking for getenv... yes
checking for __freadable... yes
checking for _sysconf... no
checking for getrusage... yes
checking for strerror... yes
checking for cbrt... no
checking for lsqrt... no
checking for vsnprintf... yes
checking for strtoul... yes
checking for strtoll... yes
checking for strtoull... yes
checking for uname... yes
checking for memset... yes
checking for nl_langinfo... yes
checking for pow... no
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... (cached) yes
checking for strstr... yes
checking for _NSGetEnviron... no
checking for strcasecmp... yes
checking for strncasecmp... yes
checking for strcasestr... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking dependency style of g++ -std=gnu++17... (cached) gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ld used by g++ -std=gnu++17... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++17 static flag -static works... yes
checking if g++ -std=gnu++17 supports -c -o file.o... yes
checking if g++ -std=gnu++17 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc options needed to detect all undeclared functions... none needed
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for ltdl.h... yes
checking whether lt_dlinterface_register is declared... yes
checking for lt_dladvise_preload in -lltdl... yes
checking where to find libltdl headers...
checking where to find libltdl library... -lltdl
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking for X... disabled
configure: WARNING: X11 not available.
using tcl headers from -I/usr/include/tcl8.6 -I/usr/include/tcl8.6/generic
checking for tcl.h... yes
using /usr/lib/tclConfig.sh
checking for wish8.6... /usr/bin/wish8.6
checking for tk.h... yes
checking for tk.h... (cached) yes
checking for tkInt.h... no
using /usr/lib/tkConfig.sh
checking for connect... yes
checking for gethostbyname... yes
checking for main in -lXpm... no
configure: WARNING: Optional Xpm library not available
checking for X11/Intrinsic.h... yes
checking for X11/Xaw/Text.h... no
configure: WARNING: Optional Xaw library not available - missing headers
checking for zlib.h... yes
checking for main in -lz... yes
checking for deflateBound... no
checking for GDK_PIXBUF... yes
checking for GTK... yes
checking for GTKGL... no
checking for GTKGLEXT... no
checking for GLADE... no
checking for qmake-qt4... no
checking for qmake-qt3... no
checking for qmake... no
checking for sincos... yes
checking if FILE struct contains _cnt... no
checking if FILE struct contains _r... no
checking if FILE struct contains _next... no
checking if FILE struct contains _IO_read_end... yes
checking if errno externs are declared... no
checking if getopt externs are declared... yes
checking if intptr_t is declared... yes
checking if assert needs __eprintf... no
checking that generated files are newer than configure... done
configure: creating ./config.status
----------------------------------------------------------------
graphviz-2.28.0 will be compiled with the following:
options:
cgraph: No (disabled by default - experimental)
digcola: Yes
expat: No (disabled)
fontconfig: No (disabled)
freetype: No (disabled)
glut: No (disabled)
gts: No (disabled)
ipsepcola: No (disabled by default - C++ portability issues)
ltdl: No (disabled)
ortho: Yes
png: No (disabled)
jpeg: No (disabled)
sfdp: Yes
shared: No (disabled)
static: Yes
qt: No (qmake not found)
commands:
dot: Yes (always enabled)
neato: Yes (always enabled)
fdp: Yes (always enabled)
circo: Yes (always enabled)
twopi: Yes (always enabled)
gvpr: Yes (always enabled)
gvmap: Yes (always enabled)
lefty: No (missing Xaw headers)
smyrna: No (disabled by default - experimental)
gvedit: No (qmake not found)
plugin libraries:
dot_layout: Yes (always enabled)
neato_layout: Yes (always enabled)
core: Yes (always enabled)
devil: No (disabled)
gd: No (disabled)
gdiplus: No (disabled by default - Windows only)
gdk_pixbuf: Yes
ghostscript: No (disabled)
glitz: No (disabled by default - incomplete)
gtk: Yes
lasi: No (disabled)
ming: No (disabled by default - incomplete)
pangocairo: No (disabled)
quartz: No (disabled by default - Mac only)
rsvg: No (disabled)
visio: No (disabled by default - experimental)
xlib: No (disabled or unavailable)
language extensions:
gv_sharp: No (swig not available)
gv_go: No (disabled by default - experimental)
gv_guile: No (swig not available)
gv_io: No (disabled by default - no swig support yet)
gv_java: No (swig not available)
gv_lua: No (swig not available)
gv_ocaml: No (swig not available)
gv_perl: No (swig not available)
gv_php: No (swig not available)
gv_python: No (swig not available)
gv_python23: No (disabled by default - for multiversion installs)
gv_python24: No (disabled by default - for multiversion installs)
gv_python25: No (disabled by default - for multiversion installs)
gv_python26: No (disabled by default - for multiversion installs)
gv_python27: No (disabled by default - for multiversion installs)
gv_R: No (swig not available)
gv_ruby: No (swig not available)
gv_tcl: No (swig not available)
tcldot: Yes
tclpathplan: Yes
gdtclft: No (gd not available)
tkspline: Yes
/bin/bash ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/config/missing --run autoheader)
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
rm -f stamp-h1
touch config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make install-recursive
make[1]: Entering directory '/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'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run aclocal-1.12 -I m4
/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system. You should only need it if
you modified `acinclude.m4' or `configure.ac'. You might want
to install the `Automake' and `Perl' packages. Grab them from
any GNU archive site.
cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run automake-1.12 --foreign
/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system. You should only need it if
you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
You might want to install the `Automake' and `Perl' packages.
Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoconf
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure --disable-option-checking --prefix=/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/libunix CC=gcc CXX=g++ -std=gnu++17 CFLAGS=-g -O2 -Wall CXXFLAGS=-g -O2 -Wall LDFLAGS=-L/usr/local/lib --libdir=/home/biocbuild/bbs-3.21-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/bbs-3.21-bioc/R/site-library/00LOCK-Rgraphviz/00new:/home/biocbuild/bbs-3.21-bioc/R/site-library --cache-file=/dev/null --srcdir=. --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu
checking for gcc options needed to detect all undeclared functions... none needed
checking for library containing dlopen... none required
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
/bin/bash ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make install-am
make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl'
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fPIC -DPIC -o dlopen.o
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -module -avoid-version -L/usr/local/lib -o dlopen.la dlopen.lo
libtool: link: ar cru .libs/dlopen.a dlopen.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/dlopen.a
libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c -fPIC -DPIC -o libltdlc_la-preopen.o
mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c -fPIC -DPIC -o libltdlc_la-lt__alloc.o
mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c -fPIC -DPIC -o libltdlc_la-lt_dlloader.o
mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c -fPIC -DPIC -o libltdlc_la-lt_error.o
mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c -fPIC -DPIC -o libltdlc_la-ltdl.o
In file included from libltdl/lt__private.h:51,
from ltdl.c:32:
ltdl.c: In function 'try_dlopen':
./ltdl.h:44:27: warning: the address of 'libext' will always evaluate as 'true' [-Waddress]
44 | #define LT_STRLEN(s) (((s) && (s)[0]) ? strlen (s) : 0)
| ^
libltdl/lt__alloc.h:38:51: note: in definition of macro 'MALLOC'
38 | #define MALLOC(tp, n) (tp*) lt__malloc((n) * sizeof(tp))
| ^
ltdl.c:1268:59: note: in expansion of macro 'LT_STRLEN'
1268 | archive_name = MALLOC (char, LT_STRLEN (name) + LT_STRLEN (libext) + 2);
| ^~~~~~~~~
mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo
/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -I/usr/local/include -g -O2 -Wall -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c -fPIC -DPIC -o libltdlc_la-slist.o
mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo
/bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -no-undefined -dlpreopen dlopen.la -L/usr/local/lib -o libltdlc.la libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo
libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT
libtool: link: (cd .libs && gcc -g -O2 -Wall -c -fno-builtin -fPIC -DPIC "libltdlcS.c")
libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT"
libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/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
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/biocbuild/bbs-3.21-bioc/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoheader)
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
rm -f stamp-h1
touch config-h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
make[4]: Entering directory '/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
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libcdt_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
/usr/bin/sed "s/yy/ag/g" < y.tab.h > parser.h
CC lexer.lo
lexer.c: In function 'scan_token':
lexer.c:141:11: warning: comparison between pointer and zero character constant [-Wpointer-compare]
141 | if (p == '\0')
| ^~
lexer.c:141:9: note: did you mean to dereference the pointer?
141 | if (p == '\0')
| ^
lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign]
147 | return p;
| ^
lexer.c: In function 'html_pair':
lexer.c:322:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
322 | int rc, depth = 1;
| ^~
In file included from lexer.c:20:
lexer.c: In function 'aglex':
agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
lexer.c:413:36: note: in expansion of macro 'agxbuse'
413 | aglval.str = agstrdup_html(agxbuse(&xb));
| ^~~~~~~
lexer.c:435:33: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign]
435 | LexPtr = scan_token(LexPtr, tbuf);
| ^~~~~~
| |
| char *
lexer.c:136:40: note: expected 'unsigned char *' but argument is of type 'char *'
136 | static char *scan_token(unsigned char *p, unsigned char *token)
| ~~~~~~~~~~~~~~~^
lexer.c:435:41: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign]
435 | LexPtr = scan_token(LexPtr, tbuf);
| ^~~~
| |
| char *
lexer.c:136:58: note: expected 'unsigned char *' but argument is of type 'char *'
136 | static char *scan_token(unsigned char *p, unsigned char *token)
| ~~~~~~~~~~~~~~~^~~~~
lexer.c: In function 'aglasterr':
lexer.c:527:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
527 | fread(buf, sizeof(char), len, agerrout);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CC node.lo
/usr/bin/sed "s/yy/ag/g" < y.tab.c > parser.c
CC parser.lo
CC refstr.lo
CC trie.lo
CCLD libgraph.la
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libgraph_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libpathplan_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
ar: `u' modifier ignored since `D' is the default (see `U')
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;
| ^~
In file included from /usr/include/stdio.h:980,
from ../../lib/common/types.h:17,
from structures.h:17,
from sgraph.h:17,
from maze.h:17,
from ortho.c:31:
In function 'fprintf',
inlined from 'putSeg' at ortho.c:545:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ortho.c: In function 'putSeg':
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
In function 'fprintf',
inlined from 'putSeg' at ortho.c:545:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ortho.c: In function 'putSeg':
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
In function 'fprintf',
inlined from 'putSeg' at ortho.c:542:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ortho.c: In function 'putSeg':
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
In function 'fprintf',
inlined from 'putSeg' at ortho.c:542:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:79:10: warning: 's' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ortho.c: In function 'putSeg':
ortho.c:518:9: note: 's' was declared here
518 | char* s;
| ^
ortho.c: In function 'orthoEdges':
ortho.c:1303:25: warning: 'ps' may be used uninitialized [-Wmaybe-uninitialized]
1303 | if (isInPS (ps,hi,ti)) continue;
| ^~~~~~~~~~~~~~~~~
ortho.c:1250:15: note: 'ps' was declared here
1250 | PointSet* ps;
| ^~
In function 'convertSPtoRoute',
inlined from 'orthoEdges' at ortho.c:1341:25:
ortho.c:179:25: warning: 'prevbp.y' may be used uninitialized [-Wmaybe-uninitialized]
179 | else if (prevbp.y > bp1.y) l1 = B_UP;
| ^
ortho.c: In function 'orthoEdges':
ortho.c:152:22: note: 'prevbp.y' was declared here
152 | pointf bp1, bp2, prevbp; /* bend points */
| ^~~~~~
In function 'convertSPtoRoute',
inlined from 'orthoEdges' at ortho.c:1341:25:
ortho.c:192:25: warning: 'prevbp.x' may be used uninitialized [-Wmaybe-uninitialized]
192 | else if (prevbp.x > bp1.x) l1 = B_RIGHT;
| ^
ortho.c: In function 'orthoEdges':
ortho.c:152:22: note: 'prevbp.x' was declared here
152 | pointf bp1, bp2, prevbp; /* bend points */
| ^~~~~~
CC partition.lo
partition.c: In function 'traverse_polygon':
partition.c:328:7: warning: variable 'do_switch' set but not used [-Wunused-but-set-variable]
328 | int do_switch = FALSE;
| ^~~~~~~~~
partition.c:327:7: warning: variable 'retval' set but not used [-Wunused-but-set-variable]
327 | int retval;
| ^~~~~~
partition.c: In function 'partition':
partition.c:731:9: warning: variable 'nt' set but not used [-Wunused-but-set-variable]
731 | int nt;
| ^~
partition.c: In function 'make_new_monotone_poly':
partition.c:298:18: warning: 'tp' may be used uninitialized [-Wmaybe-uninitialized]
298 | vp0->vnext[ip] = v1;
| ~~~~~~~~~~~~~~~^~~~
partition.c:212:7: note: 'tp' was declared here
212 | int tp, tq;
| ^~
partition.c:274:5: warning: 'tq' may be used uninitialized [-Wmaybe-uninitialized]
274 | q = vp1->vpos[iq];
| ~~^~~~~~~~~~~~~~~
partition.c:212:11: note: 'tq' was declared here
212 | int tp, tq;
| ^~
partition.c: In function 'monotonate_trapezoids':
partition.c:665:10: warning: 'size' may be used uninitialized [-Wmaybe-uninitialized]
665 | return size;
| ^~~~
partition.c:620:12: note: 'size' was declared here
620 | int i, size;
| ^~~~
CC rawgraph.lo
CC sgraph.lo
CC trapezoid.lo
trapezoid.c:22: warning: "__USE_ISOC99" redefined
22 | #define __USE_ISOC99
|
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/string.h:26,
from trapezoid.c:19:
/usr/include/features.h:347: note: this is the location of the previous definition
347 | # define __USE_ISOC99 1
|
trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
66 | static int newnode()
| ^~~~~~~
trapezoid.c: In function 'add_segment':
trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable]
437 | int tritop = 0, tribot = 0, is_swapped;
| ^~~~~~
trapezoid.c: In function 'add_segment.isra':
trapezoid.c:996:3: warning: 'tfirstr' may be used uninitialized [-Wmaybe-uninitialized]
996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trapezoid.c:434:7: note: 'tfirstr' was declared here
434 | int tfirstr, tlastr, tfirstl, tlastl;
| ^~~~~~~
trapezoid.c:996:3: warning: 'tlastr' may be used uninitialized [-Wmaybe-uninitialized]
996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trapezoid.c:434:16: note: 'tlastr' was declared here
434 | int tfirstr, tlastr, tfirstl, tlastl;
| ^~~~~~
CCLD libortho_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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;
| ^~~~
cat brewer_lib svgcolor_lib ../../lib/common/color_names | LC_ALL=C sort > color_lib
gawk -f ../../awk/colortbl.awk color_lib > colortbl.h
CC colxlate.lo
CC fontmetrics.lo
CC args.lo
CC memory.lo
CC globals.lo
/usr/bin/sed "s/yy/html/g" < y.tab.h > htmlparse.h
CC htmllex.lo
In file included from render.h:47,
from htmllex.c:15:
htmllex.c: In function 'error_context':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
htmllex.c:57:35: note: in expansion of macro 'agxbuse'
57 | agerr(AGPREV, "... %s ...\n", agxbuse(state.xb));
| ^~~~~~~
/usr/bin/sed "s/yy/html/g" < y.tab.c > htmlparse.c
CC htmlparse.lo
In file included from render.h:47,
from ../../lib/common/htmlparse.y:16:
../../lib/common/htmlparse.y: In function 'appendFItemList':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
../../lib/common/htmlparse.y:193:25: note: in expansion of macro 'agxbuse'
193 | fi->ti.str = strdup(agxbuse(ag));
| ^~~~~~~
../../lib/common/htmlparse.y: In function 'htmlparse':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
../../lib/common/htmlparse.y:500:24: note: in expansion of macro 'agxbuse'
500 | if (nonSpace(agxbuse(HTMLstate.str))) {
| ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
../../lib/common/htmlparse.y:511:24: note: in expansion of macro 'agxbuse'
511 | if (nonSpace(agxbuse(HTMLstate.str))) {
| ^~~~~~~
CC htmltable.lo
In file included from render.h:47,
from htmltable.c:35:
htmltable.c: In function 'initAnchor':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
htmltable.c:299:14: note: in expansion of macro 'agxbuse'
299 | id = agxbuse (&xb);
| ^~~~~~~
htmltable.c: In function 'nameOf':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
htmltable.c:1665:12: note: in expansion of macro 'agxbuse'
1665 | return agxbuse(xb);
| ^~~~~~~
htmltable.c: In function 'make_html_label':
htmltable.c:1828:12: warning: 'env.g' may be used uninitialized [-Wmaybe-uninitialized]
1828 | g = env.g->root;
| ~~~^~
htmltable.c:1809:15: note: 'env' declared here
1809 | htmlenv_t env;
| ^~~
CC input.lo
input.c: In function 'dotneato_basename':
input.c:136:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation]
136 | while (*s) s++; s--;
| ^~~~~
input.c:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while'
136 | while (*s) s++; s--;
| ^
In file included from render.h:47,
from input.c:15:
input.c: In function 'global_def':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
input.c:200:24: note: in expansion of macro 'agxbuse'
200 | sym = dclfun(NULL, agxbuse (xb), rhs);
| ^~~~~~~
CC pointset.lo
CC postproc.lo
CC routespl.lo
CC splines.lo
CC psusershape.lo
psusershape.c: In function 'user_init':
psusershape.c:49:30: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
49 | int saw_bb, must_inline, rc;
| ^~
In file included from render.h:47,
from psusershape.c:20:
psusershape.c: In function 'ps_string':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
psusershape.c:303:5: note: in expansion of macro 'agxbputc'
303 | agxbputc (&xb, RPAREN);
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
psusershape.c:305:9: note: in expansion of macro 'agxbuse'
305 | s = agxbuse(&xb);
| ^~~~~~~
psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
268 | int rc;
| ^~
CC timing.lo
CC labels.lo
labels.c: In function 'xml_url_string':
labels.c:561:21: warning: variable 'prev' set but not used [-Wunused-but-set-variable]
561 | char *p, *sub, *prev = NULL;
| ^~~~
CC ns.lo
CC shapes.lo
CC utils.lo
utils.c: In function 'chkPort':
utils.c:690:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
690 | else
| ^~~~
utils.c:692:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
692 | pt.name = s;
| ^~
In file included from render.h:47,
from utils.c:14:
utils.c: In function 'clustNode':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:950:5: note: in expansion of macro 'agxbputc'
950 | agxbputc(xb, ':');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
utils.c:954:29: note: in expansion of macro 'agxbuse'
954 | cn = agnode(agroot(cg), agxbuse(xb));
| ^~~~~~~
utils.c: In function 'scanEntity':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:1359:5: note: in expansion of macro 'agxbputc'
1359 | agxbputc(xb, '&');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:1369:5: note: in expansion of macro 'agxbputc'
1369 | agxbputc(xb, '#');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
utils.c:1371:5: note: in expansion of macro 'agxbputc'
1371 | agxbputc(xb, ';');
| ^~~~~~~~
utils.c: In function 'htmlEntityUTF8':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
utils.c:1515:18: note: in expansion of macro 'agxbuse'
1515 | ns = strdup (agxbuse(&xb));
| ^~~~~~~
utils.c:1456:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
1456 | int rc;
| ^~
utils.c: In function 'latin1ToUTF8':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
utils.c:1555:18: note: in expansion of macro 'agxbuse'
1555 | ns = strdup (agxbuse(&xb));
| ^~~~~~~
utils.c:1531:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
1531 | int rc;
| ^~
utils.c: In function 'utf8ToLatin1':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
utils.c:1587:18: note: in expansion of macro 'agxbuse'
1587 | ns = strdup (agxbuse(&xb));
| ^~~~~~~
utils.c:1573:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
1573 | int rc;
| ^~
CC geom.lo
CC output.lo
In file included from render.h:47,
from output.c:14:
output.c: In function 'attach_attrs_and_arrows':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
output.c:350:29: note: in expansion of macro 'agxbuse'
350 | agset(n, "pos", agxbuse(&xb));
| ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
output.c:373:31: note: in expansion of macro 'agxbuse'
373 | agset(n, "rects", agxbuse(&xb));
| ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.c:391:25: note: in expansion of macro 'agxbputc'
391 | agxbputc(&xb, ' ');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
output.c:403:46: note: in expansion of macro 'agxbuse'
403 | agxset(n, N_vertices->index, agxbuse(&xb));
| ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.c:417:25: note: in expansion of macro 'agxbputc'
417 | agxbputc(&xb, ';');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
output.c:434:29: note: in expansion of macro 'agxbputc'
434 | agxbputc(&xb, ' ');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
output.c:440:33: note: in expansion of macro 'agxbuse'
440 | agset(e, "pos", agxbuse(&xb));
| ^~~~~~~
CC emit.lo
In file included from render.h:47,
from emit.c:25:
emit.c: In function 'getObjId':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:212:9: note: in expansion of macro 'agxbputc'
212 | agxbputc (xb, '_');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
emit.c:218:12: note: in expansion of macro 'agxbuse'
218 | return agxbuse(xb);
| ^~~~~~~
emit.c: In function 'emit_xdot':
emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable]
941 | char* fontname;
| ^~~~~~~~
emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable]
940 | double fontsize;
| ^~~~~~~~
emit.c: In function 'selectedlayer':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
emit.c:1152:22: note: in expansion of macro 'agxbuse'
1152 | w1 = w0 = strtok(agxbuse(&xb), gvc->layerDelims);
| ^~~~~~~
emit.c: In function 'nodeIntersect':
emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
2247 | char* target;
| ^~~~~~
emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable]
2246 | char* tooltip;
| ^~~~~~~
emit.c: In function 'xdotBB':
emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable]
2474 | pointf sz;
| ^~
emit.c: In function 'style_token':
emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable]
3262 | int token, rc;
| ^~
emit.c: In function 'parse_style':
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:3356:17: note: in expansion of macro 'agxbputc'
3356 | agxbputc(&ps_xb, '\0'); /* terminate previous */
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
emit.c:3359:29: note: in expansion of macro 'agxbuse'
3359 | agxbput(&ps_xb, agxbuse(&xb));
| ^~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:3360:13: note: in expansion of macro 'agxbputc'
3360 | agxbputc(&ps_xb, '\0');
| ^~~~~~~~
../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value]
68 | (int)(*(X)->ptr++ = ((unsigned char)C)))
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc'
74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf))
| ^~~~~~~~
emit.c:3372:11: note: in expansion of macro 'agxbuse'
3372 | (void)agxbuse(&ps_xb); /* adds final '\0' to buffer */
| ^~~~~~~
In file included from /usr/include/stdio.h:980,
from types.h:17,
from render.h:40:
In function 'sprintf',
inlined from 'getObjId' at emit.c:215:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: 'idnum' may be used uninitialized [-Wmaybe-uninitialized]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
emit.c: In function 'getObjId':
emit.c:182:10: note: 'idnum' was declared here
182 | long idnum;
| ^~~~~
emit.c:214:5: warning: 'pfx' may be used uninitialized [-Wmaybe-uninitialized]
214 | agxbput (xb, pfx);
| ^~~~~~~~~~~~~~~~~
emit.c:183:11: note: 'pfx' was declared here
183 | char* pfx;
| ^~~
emit.c: In function 'xdotBB':
emit.c:2515:18: warning: 'fontsize' may be used uninitialized [-Wmaybe-uninitialized]
2515 | sz = textsize (g, op->para, fontname, fontsize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:2471:12: note: 'fontsize' was declared here
2471 | double fontsize;
| ^~~~~~~~
emit.c:2515:18: warning: 'fontname' may be used uninitialized [-Wmaybe-uninitialized]
2515 | sz = textsize (g, op->para, fontname, fontsize);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c:2472:11: note: 'fontname' was declared here
2472 | char* fontname;
| ^~~~~~~~
In function 'multicolor',
inlined from 'emit_edge_graphics' at emit.c:1814:10,
inlined from 'emit_edge' at emit.c:2389:2,
inlined from 'emit_edge' at emit.c:2350:13:
emit.c:1776:13: warning: 'endcolor' may be used uninitialized [-Wmaybe-uninitialized]
1776 | gvrender_set_fillcolor(job, endcolor);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c: In function 'emit_edge':
emit.c:1723:11: note: 'endcolor' was declared here
1723 | char* endcolor;
| ^~~~~~~~
In function 'emit_edge_graphics',
inlined from 'emit_edge' at emit.c:2389:2,
inlined from 'emit_edge' at emit.c:2350:13:
emit.c:1921:17: warning: 'bz.list' may be used uninitialized [-Wmaybe-uninitialized]
1921 | arrow_gen(job, EMIT_TDRAW, bz.sp, bz.list[0],
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1922 | arrowsize, penwidth, bz.sflag);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
emit.c: In function 'emit_edge':
emit.c:1792:12: note: 'bz.list' was declared here
1792 | bezier bz;
| ^~
In function 'emit_edge_graphics',
inlined from 'emit_edge' at emit.c:2389:2,
inlined from 'emit_edge' at emit.c:2350:13:
emit.c:1932:61: warning: 'bz.size' may be used uninitialized [-Wmaybe-uninitialized]
1932 | arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1],
| ~~^~~~~
emit.c: In function 'emit_edge':
emit.c:1792:12: note: 'bz.size' was declared here
1792 | bezier bz;
| ^~
In function 'emit_edge_graphics',
inlined from 'emit_edge' at emit.c:2389:2,
inlined from 'emit_edge' at emit.c:2350:13:
emit.c:1913:16: warning: 'bz.sflag' may be used uninitialized [-Wmaybe-uninitialized]
1913 | if (bz.sflag) {
| ^
emit.c: In function 'emit_edge':
emit.c:1792:12: note: 'bz.sflag' was declared here
1792 | bezier bz;
| ^~
In function 'emit_edge_graphics',
inlined from 'emit_edge' at emit.c:2389:2,
inlined from 'emit_edge' at emit.c:2350:13:
emit.c:1924:16: warning: 'bz.eflag' may be used uninitialized [-Wmaybe-uninitialized]
1924 | if (bz.eflag) {
| ^
emit.c: In function 'emit_edge':
emit.c:1792:12: note: 'bz.eflag' was declared here
1792 | bezier bz;
| ^~
CCLD libcommon_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libxdot_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libgvc_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
ar: `u' modifier ignored since `D' is the default (see `U')
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;
| ^~
dotsplines.c: In function '_dot_splines':
dotsplines.c:882:12: warning: 'lminx' may be used uninitialized [-Wmaybe-uninitialized]
882 | double lminx, lmaxx;
| ^~~~~
dotsplines.c:882:19: warning: 'lmaxx' may be used uninitialized [-Wmaybe-uninitialized]
882 | double lminx, lmaxx;
| ^~~~~
dotsplines.c:488:9: warning: 'edges' may be used uninitialized [-Wmaybe-uninitialized]
488 | free(edges);
| ^~~~~~~~~~~
dotsplines.c:268:50: note: 'edges' was declared here
268 | edge_t *e, *e0, *e1, *ea, *eb, *le0, *le1, **edges;
| ^~~~~
dotsplines.c:489:15: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized]
489 | free(P->boxes);
| ~^~~~~~~
dotsplines.c:269:11: note: 'P' was declared here
269 | path *P;
| ^
CC aspect.lo
aspect.c: In function 'computeCombiAR':
aspect.c:1614:12: warning: variable 'maxLayerIndex' set but not used [-Wunused-but-set-variable]
1614 | int i, maxLayerIndex;
| ^~~~~~~~~~~~~
In function 'reduceMaxWidth2',
inlined from 'applyPacking2' at aspect.c:1088:5,
inlined from 'rank3' at aspect.c:1824:2:
aspect.c:737:25: warning: 'maxLayerIndex' may be used uninitialized [-Wmaybe-uninitialized]
737 | layerWidthInfo[maxLayerIndex].nNodeGroupsInLayer,
| ^
aspect.c: In function 'rank3':
aspect.c:702:9: note: 'maxLayerIndex' was declared here
702 | int maxLayerIndex;
| ^~~~~~~~~~~~~
In function 'reduceMaxWidth2',
inlined from 'applyPacking2' at aspect.c:1088:5,
inlined from 'rank3' at aspect.c:1824:2:
aspect.c:749:8: warning: 'nextMaxWidth' may be used uninitialized [-Wmaybe-uninitialized]
749 | if (nextMaxWidth <= layerWidthInfo[maxLayerIndex].width / 4
| ^
aspect.c: In function 'rank3':
aspect.c:703:12: note: 'nextMaxWidth' was declared here
703 | double nextMaxWidth;
| ^~~~~~~~~~~~
CCLD libdotgen_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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 <unistd.h> # for read() declaration
| ^
CCLD libgvplugin_core_C.la
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libgvplugin_core.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libgvplugin_dot_layout.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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
ar: `u' modifier ignored since `D' is the default (see `U')
CCLD libgvplugin_neato_layout.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Entering directory '/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/bash ../../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/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/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: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c LL_funcs.c -o LL_funcs.o
LL_funcs.c: In function ‘Rgraphviz_agopenSimple’:
LL_funcs.c:430:29: warning: variable ‘curNode’ set but not used [-Wunused-but-set-variable]
430 | Agnode_t *head, *tail, *curNode;
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c Rgraphviz.c -o Rgraphviz.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c RgraphvizInit.c -o RgraphvizInit.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c agopen.c -o agopen.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c agread.c -o agread.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c agwrite.c -o agwrite.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c bezier.c -o bezier.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c buildEdgeList.c -o buildEdgeList.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c buildNodeList.c -o buildNodeList.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c doLayout.c -o doLayout.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c graphvizVersion.c -o graphvizVersion.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -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 -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-Rgraphviz/00new/Rgraphviz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rgraphviz)
Rgraphviz.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("Rgraphviz") || stop("unable to load Rgraphviz")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: grid
[1] TRUE
> BiocGenerics:::testPackage("Rgraphviz")
plotting different layout types
dot .... done
circo .... done
fdp .... done
neato .... done
osage .... done
twopi .... done
using toFile with various device types
canon . done
cmap . done
cmapx . done
cmapx_np . done
dot . done
eps . done
fig . done
gv . done
imap . done
imap_np . done
ismap . done
plain . done
plain-ext . done
ps . done
ps2 . done
svg . done
tk . done
vml . done
xdot . done
RUNIT TEST PROTOCOL -- Thu Nov 28 05:09:00 2024
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rgraphviz RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.003 0.067 1.060
Rgraphviz.Rcheck/Rgraphviz-Ex.timings
| name | user | system | elapsed | |
| AgEdge-class | 0.047 | 0.013 | 0.060 | |
| AgNode-class | 0.005 | 0.000 | 0.005 | |
| AgTextLabel-class | 0.007 | 0.001 | 0.008 | |
| BezierCurve-class | 0.004 | 0.001 | 0.005 | |
| GraphvizLayouts | 0.001 | 0.001 | 0.002 | |
| Ragraph-class | 0.016 | 0.007 | 0.022 | |
| agopen | 0.006 | 0.001 | 0.007 | |
| agopenSimple | 0.043 | 0.000 | 0.043 | |
| agwrite | 0.005 | 0.000 | 0.005 | |
| boundingBox-class | 0.004 | 0.001 | 0.004 | |
| buildNodeList | 0.002 | 0.000 | 0.002 | |
| clusterData-methods | 0.153 | 0.003 | 0.156 | |
| getDefaultAttrs | 0.001 | 0.000 | 0.001 | |
| graphLayout | 0.004 | 0.000 | 0.003 | |
| graphvizCapabilities | 0.000 | 0.001 | 0.001 | |
| graphvizVersion | 0.001 | 0.000 | 0.001 | |
| layoutGraph | 0.151 | 0.000 | 0.151 | |
| makeNodeAttrs | 0.002 | 0.001 | 0.002 | |
| pEdge-class | 0.002 | 0.001 | 0.003 | |
| pNode-class | 0.002 | 0.000 | 0.002 | |
| pieGlyph | 0.005 | 0.001 | 0.006 | |
| plot-methods | 0.000 | 0.000 | 0.001 | |
| removedEdges | 0.004 | 0.001 | 0.005 | |
| renderGraph | 0.053 | 0.001 | 0.054 | |
| toDot-methods | 0.007 | 0.000 | 0.009 | |
| toFile | 0.020 | 0.000 | 0.021 | |
| xyPoint-class | 0.001 | 0.000 | 0.001 | |