| Back to Rapid builds (Linux only) of a subset of BioC 3.21 Report updated every 6 hours |
This page was generated on 2025-04-01 18:16 -0400 (Tue, 01 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 871 |
| 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 170/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| Rgraphviz 2.51.9 (landing page) Kasper Daniel Hansen
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
|
To the developers/maintainers of the Rgraphviz package: - 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: 2.51.9 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL Rgraphviz |
| StartedAt: 2025-04-01 18:05:20 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 18:05:56 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 36.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL Rgraphviz
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘Rgraphviz’ ...
** this is package ‘Rgraphviz’ version ‘2.51.9’
** using staged installation
configure: Using bundled Graphviz.
configure: Searching for the compilers specified by R.
checking for gcc... gcc -std=gnu17
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 -std=gnu17 accepts -g... yes
checking for gcc -std=gnu17 option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -std=gnu17 -E
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... -std=gnu++11
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 -std=gnu17
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 -std=gnu17 accepts -g... yes
checking for gcc -std=gnu17 option to accept ISO C89... none needed
checking dependency style of gcc -std=gnu17... gcc3
checking for library containing strerror... none required
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
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checking for ps2pdf... ps2pdf
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checking dependency style of g++ -std=gnu++11... gcc3
checking for gcc... gcc
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checking for inline... inline
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checking how to run the C preprocessor... gcc -std=gnu17 -E
checking for grep that handles long lines and -e... grep
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checking sys/fpu.h usability... no
checking sys/fpu.h presence... no
checking for sys/fpu.h... no
checking sys/socket.h usability... no
checking sys/socket.h presence... yes
configure: WARNING: sys/socket.h: present but cannot be compiled
configure: WARNING: sys/socket.h: check for missing prerequisite headers?
configure: WARNING: sys/socket.h: see the Autoconf documentation
configure: WARNING: sys/socket.h: section "Present But Cannot Be Compiled"
configure: WARNING: sys/socket.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for sys/socket.h... no
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... no
checking sys/mman.h presence... yes
configure: WARNING: sys/mman.h: present but cannot be compiled
configure: WARNING: sys/mman.h: check for missing prerequisite headers?
configure: WARNING: sys/mman.h: see the Autoconf documentation
configure: WARNING: sys/mman.h: section "Present But Cannot Be Compiled"
configure: WARNING: sys/mman.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for sys/mman.h... no
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checking sys/ioctl.h presence... yes
configure: WARNING: sys/ioctl.h: present but cannot be compiled
configure: WARNING: sys/ioctl.h: check for missing prerequisite headers?
configure: WARNING: sys/ioctl.h: see the Autoconf documentation
configure: WARNING: sys/ioctl.h: section "Present But Cannot Be Compiled"
configure: WARNING: sys/ioctl.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for sys/ioctl.h... no
checking sys/inotify.h usability... no
checking sys/inotify.h presence... yes
configure: WARNING: sys/inotify.h: present but cannot be compiled
configure: WARNING: sys/inotify.h: check for missing prerequisite headers?
configure: WARNING: sys/inotify.h: see the Autoconf documentation
configure: WARNING: sys/inotify.h: section "Present But Cannot Be Compiled"
configure: WARNING: sys/inotify.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for sys/inotify.h... no
checking langinfo.h usability... no
checking langinfo.h presence... yes
configure: WARNING: langinfo.h: present but cannot be compiled
configure: WARNING: langinfo.h: check for missing prerequisite headers?
configure: WARNING: langinfo.h: see the Autoconf documentation
configure: WARNING: langinfo.h: section "Present But Cannot Be Compiled"
configure: WARNING: langinfo.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for langinfo.h... no
checking libintl.h usability... no
checking libintl.h presence... yes
configure: WARNING: libintl.h: present but cannot be compiled
configure: WARNING: libintl.h: check for missing prerequisite headers?
configure: WARNING: libintl.h: see the Autoconf documentation
configure: WARNING: libintl.h: section "Present But Cannot Be Compiled"
configure: WARNING: libintl.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for libintl.h... no
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checking for crt_externs.h... no
checking whether time.h and sys/time.h may both be included... no
checking for dirent.h that defines DIR... no
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checking for stdbool.h that conforms to C99... no
checking for _Bool... no
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checking libgen.h usability... no
checking libgen.h presence... yes
configure: WARNING: libgen.h: present but cannot be compiled
configure: WARNING: libgen.h: check for missing prerequisite headers?
configure: WARNING: libgen.h: see the Autoconf documentation
configure: WARNING: libgen.h: section "Present But Cannot Be Compiled"
configure: WARNING: libgen.h: proceeding with the compiler's result
configure: WARNING: ## --------------------------------------- ##
configure: WARNING: ## Report this to http://www.graphviz.org/ ##
configure: WARNING: ## --------------------------------------- ##
checking for libgen.h... no
configure: WARNING: libgen.h header not available
checking for working alloca.h... no
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checking whether `alloca.c' needs Cray hooks... no
checking stack direction for C alloca... -1
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checking for fgrep... grep -F
checking for ld used by gcc -std=gnu17... /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 -std=gnu17 object... failed
checking for dlfcn.h... no
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking dependency style of g++ -std=gnu++11... (cached) gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for objdir... .libs
checking if gcc -std=gnu17 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu17 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu17 PIC flag -fPIC -DPIC works... no
checking if gcc -std=gnu17 static flag -static works... no
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checking if gcc -std=gnu17 supports -c -o file.o... (cached) no
checking if we can lock with hard links... yes
checking whether the gcc -std=gnu17 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking whether stripping libraries is possible... yes
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checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... yes
checking if g++ -std=gnu++11 supports -c -o file.o... yes
checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/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
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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
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using /usr/lib/tclConfig.sh
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using /usr/lib/tkConfig.sh
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checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix' 'CC=gcc -std=gnu17' 'CXX=g++ -std=gnu++11' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2 -Wall -Werror=format-security' 'LDFLAGS=-L/usr/local/lib' '--libdir=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/lib' '--includedir=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'CPPFLAGS=-I/usr/local/include' 'R_LIBS=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-Rgraphviz/00new:/home/rapidbuild/bbs-3.21-bioc-rapid/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 -std=gnu17
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 -std=gnu17 accepts -g... yes
checking for gcc -std=gnu17 option to accept ISO C89... none needed
checking dependency style of gcc -std=gnu17... 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 -std=gnu17... /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 -std=gnu17 object... ok
checking how to run the C preprocessor... gcc -std=gnu17 -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 -std=gnu17 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu17 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu17 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu17 static flag -static works... yes
checking if gcc -std=gnu17 supports -c -o file.o... yes
checking if gcc -std=gnu17 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu17 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
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checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
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checking if argz actually works... yes
checking whether libtool supports -dlopen/-dlpreopen... yes
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checking for closedir... yes
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checking for readdir... yes
checking for strlcat... yes
checking for strlcpy... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
----------------------------------------------------------------
graphviz-2.28.0 will be compiled with the following:
options:
cgraph: No (disabled by default - experimental)
digcola: Yes
expat: No (disabled)
fontconfig: No (disabled)
freetype: No (disabled)
glut: No (disabled)
gts: No (disabled)
ipsepcola: No (disabled by default - C++ portability issues)
ltdl: No (disabled)
ortho: Yes
png: No (disabled)
jpeg: No (disabled)
sfdp: Yes
shared: No (disabled)
static: Yes
qt: No (qmake not found)
commands:
dot: Yes (always enabled)
neato: Yes (always enabled)
fdp: Yes (always enabled)
circo: Yes (always enabled)
twopi: Yes (always enabled)
gvpr: Yes (always enabled)
gvmap: Yes (always enabled)
lefty: Yes
smyrna: No (disabled by default - experimental)
gvedit: No (qmake not found)
plugin libraries:
dot_layout: Yes (always enabled)
neato_layout: Yes (always enabled)
core: Yes (always enabled)
devil: No (disabled)
gd: No (disabled)
gdiplus: No (disabled by default - Windows only)
gdk_pixbuf: Yes
ghostscript: No (disabled)
glitz: No (disabled by default - incomplete)
gtk: Yes
lasi: No (disabled)
ming: No (disabled by default - incomplete)
pangocairo: No (disabled)
quartz: No (disabled by default - Mac only)
rsvg: No (disabled)
visio: No (disabled by default - experimental)
xlib: No (disabled or unavailable)
language extensions:
gv_sharp: No (swig not available)
gv_go: No (disabled by default - experimental)
gv_guile: No (swig not available)
gv_io: No (disabled by default - no swig support yet)
gv_java: No (swig not available)
gv_lua: No (swig not available)
gv_ocaml: No (swig not available)
gv_perl: No (swig not available)
gv_php: No (swig not available)
gv_python: No (swig not available)
gv_python23: No (disabled by default - for multiversion installs)
gv_python24: No (disabled by default - for multiversion installs)
gv_python25: No (disabled by default - for multiversion installs)
gv_python26: No (disabled by default - for multiversion installs)
gv_python27: No (disabled by default - for multiversion installs)
gv_R: No (swig not available)
gv_ruby: No (swig not available)
gv_tcl: No (swig not available)
tcldot: Yes
tclpathplan: Yes
gdtclft: No (gd not available)
tkspline: Yes
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/config/missing --run aclocal-1.12 -I m4
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system. You should only need it if
you modified `acinclude.m4' or `configure.ac'. You might want
to install the `Automake' and `Perl' packages. Grab them from
any GNU archive site.
cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/config/missing --run automake-1.12 --gnu
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system. You should only need it if
you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
You might want to install the `Automake' and `Perl' packages.
Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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...
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configure.ac:2722: You should run autoupdate.
./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
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configure.ac:2722: the top level
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configure.ac:2722: You should run autoupdate.
./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from...
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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 -std=gnu17 CXX=g++ -std=gnu++11 CFLAGS=-g -O2 CXXFLAGS=-g -O2 -Wall -Werror=format-security LDFLAGS=-L/usr/local/lib --prefix=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix --libdir=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/lib --includedir=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/include --with-cgraph=no --enable-swig=no --enable-static --disable-shared --with-pic --with-libgd=no --disable-ltdl --without-x --without-expat --without-devil --without-rsvg --without-ghostscript --without-visio --without-pangocairo --without-lasi --without-glitz --without-freetype2 --without-fontconfig --without-rpat --without-glut --without-gts --without-png --without-tcl --without-jpeg CPPFLAGS=-I/usr/local/include R_LIBS=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-Rgraphviz/00new:/home/rapidbuild/bbs-3.21-bioc-rapid/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
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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 -std=gnu17
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checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking whether the compiler supports GNU C... yes
checking whether gcc -std=gnu17 accepts -g... yes
checking for gcc -std=gnu17 option to enable C11 features... none needed
checking dependency style of gcc -std=gnu17... gcc3
checking for library containing strerror... none required
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checking for lex output file root... lex.yy
checking for lex library... none needed
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checking whether gcc -std=gnu17 and cc understand -c and -o together... yes
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checking for g++ -std=gnu++11 option to enable C++11 features... none needed
checking dependency style of g++ -std=gnu++11... gcc3
checking for gcc... gcc
checking whether the compiler supports GNU Objective C... yes
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checking dependency style of gcc... gcc3
checking for inline... inline
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checking how to run the C preprocessor... gcc -std=gnu17 -E
checking for grep that handles long lines and -e... grep
checking for egrep... grep -E
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checking if the linker (/usr/bin/ld) is GNU ld... yes
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checking command to parse /usr/bin/nm -B output from gcc -std=gnu17 object... ok
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checking for g++ -std=gnu++11 option to enable C++11 features... (cached) none needed
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checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
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checking whether the gcc -std=gnu17 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
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checking for ld used by g++ -std=gnu++11... /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++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... yes
checking if g++ -std=gnu++11 supports -c -o file.o... yes
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checking whether the g++ -std=gnu++11 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
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checking for library containing dlopen... none required
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configure: WARNING: X11 not available.
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checking that generated files are newer than configure... done
configure: creating ./config.status
----------------------------------------------------------------
graphviz-2.28.0 will be compiled with the following:
options:
cgraph: No (disabled by default - experimental)
digcola: Yes
expat: No (disabled)
fontconfig: No (disabled)
freetype: No (disabled)
glut: No (disabled)
gts: No (disabled)
ipsepcola: No (disabled by default - C++ portability issues)
ltdl: No (disabled)
ortho: Yes
png: No (disabled)
jpeg: No (disabled)
sfdp: Yes
shared: No (disabled)
static: Yes
qt: No (qmake not found)
commands:
dot: Yes (always enabled)
neato: Yes (always enabled)
fdp: Yes (always enabled)
circo: Yes (always enabled)
twopi: Yes (always enabled)
gvpr: Yes (always enabled)
gvmap: Yes (always enabled)
lefty: Yes
smyrna: No (disabled by default - experimental)
gvedit: No (qmake not found)
plugin libraries:
dot_layout: Yes (always enabled)
neato_layout: Yes (always enabled)
core: Yes (always enabled)
devil: No (disabled)
gd: No (disabled)
gdiplus: No (disabled by default - Windows only)
gdk_pixbuf: Yes
ghostscript: No (disabled)
glitz: No (disabled by default - incomplete)
gtk: Yes
lasi: No (disabled)
ming: No (disabled by default - incomplete)
pangocairo: No (disabled)
quartz: No (disabled by default - Mac only)
rsvg: No (disabled)
visio: No (disabled by default - experimental)
xlib: No (disabled or unavailable)
language extensions:
gv_sharp: No (swig not available)
gv_go: No (disabled by default - experimental)
gv_guile: No (swig not available)
gv_io: No (disabled by default - no swig support yet)
gv_java: No (swig not available)
gv_lua: No (swig not available)
gv_ocaml: No (swig not available)
gv_perl: No (swig not available)
gv_php: No (swig not available)
gv_python: No (swig not available)
gv_python23: No (disabled by default - for multiversion installs)
gv_python24: No (disabled by default - for multiversion installs)
gv_python25: No (disabled by default - for multiversion installs)
gv_python26: No (disabled by default - for multiversion installs)
gv_python27: No (disabled by default - for multiversion installs)
gv_R: No (swig not available)
gv_ruby: No (swig not available)
gv_tcl: No (swig not available)
tcldot: Yes
tclpathplan: Yes
gdtclft: No (gd not available)
tkspline: Yes
/bin/bash ./config.status
config.status: creating Makefile
config.status: creating lib/Makefile
config.status: creating lib/cdt/Makefile
config.status: creating lib/cdt/libcdt.pc
config.status: creating lib/graph/Makefile
config.status: creating lib/graph/libgraph.pc
config.status: creating lib/rbtree/Makefile
config.status: creating lib/pathplan/Makefile
config.status: creating lib/pathplan/libpathplan.pc
config.status: creating lib/dotgen/Makefile
config.status: creating lib/neatogen/Makefile
config.status: creating lib/fdpgen/Makefile
config.status: creating lib/sparse/Makefile
config.status: creating lib/sfdpgen/Makefile
config.status: creating lib/osage/Makefile
config.status: creating lib/circogen/Makefile
config.status: creating lib/twopigen/Makefile
config.status: creating lib/patchwork/Makefile
config.status: creating lib/pack/Makefile
config.status: creating lib/ortho/Makefile
config.status: creating lib/common/Makefile
config.status: creating lib/vpsc/Makefile
config.status: creating lib/gvc/Makefile
config.status: creating lib/gvc/libgvc.pc
config.status: creating lib/xdot/Makefile
config.status: creating lib/xdot/libxdot.pc
config.status: creating plugin/Makefile
config.status: creating plugin/core/Makefile
config.status: creating plugin/dot_layout/Makefile
config.status: creating plugin/neato_layout/Makefile
config.status: creating graphviz.spec
config.status: creating Doxyfile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/config/missing --run autoheader)
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
rm -f stamp-h1
touch config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h
make install-recursive
make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz'
Making install in libltdl
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run aclocal-1.12 -I m4
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: aclocal-1.12: command not found
WARNING: `aclocal-1.12' is missing on your system. You should only need it if
you modified `acinclude.m4' or `configure.ac'. You might want
to install the `Automake' and `Perl' packages. Grab them from
any GNU archive site.
cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run automake-1.12 --foreign
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl/config/missing: line 52: automake-1.12: command not found
WARNING: `automake-1.12' is missing on your system. You should only need it if
you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
You might want to install the `Automake' and `Perl' packages.
Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl/config/missing --run autoconf
aclocal.m4:16: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
configure.ac:67: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from...
./lib/autoconf/general.m4:2894: _AC_LINK_IFELSE is expanded from...
./lib/autoconf/general.m4:2911: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4161: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5236: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:67: the top level
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure --disable-option-checking --prefix=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix CC=gcc -std=gnu17 CXX=g++ -std=gnu++11 CFLAGS=-g -O2 CXXFLAGS=-g -O2 -Wall -Werror=format-security LDFLAGS=-L/usr/local/lib --libdir=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/lib --includedir=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/include --with-cgraph=no --enable-swig=no --enable-static --disable-shared --with-pic --with-libgd=no --disable-ltdl --without-x --without-expat --without-devil --without-rsvg --without-ghostscript --without-visio --without-pangocairo --without-lasi --without-glitz --without-freetype2 --without-fontconfig --without-rpat --without-glut --without-gts --without-png --without-tcl --without-jpeg CPPFLAGS=-I/usr/local/include R_LIBS=/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-Rgraphviz/00new:/home/rapidbuild/bbs-3.21-bioc-rapid/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... config.guess: cannot create a temporary directory in /tmp
configure: error: cannot guess build type; you must specify one
make[2]: *** [Makefile:440: config.status] Error 1
make[2]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz/libltdl'
make[1]: *** [Makefile:743: install-recursive] Error 1
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/graphviz'
make: *** [Makefile:1106: install] Error 2
cp: cannot stat '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/lib/*': No such file or directory
cp: cannot stat '/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/lib/graphviz/*': No such file or directory
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 or later... yes
checking for whether compiler has bool... yes
configure: Using the following compilation and linking flags for Rgraphviz
configure: PKG_CFLAGS= -I/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c LL_funcs.c -o LL_funcs.o
In file included from LL_funcs.c:1:
common.h:16:10: fatal error: gvc.h: No such file or directory
16 | #include <gvc.h>
| ^~~~~~~
compilation terminated.
make: *** [/home/rapidbuild/bbs-3.21-bioc-rapid/R/etc/Makeconf:195: LL_funcs.o] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rgraphviz’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rgraphviz’