Question: Rgraphviz installation issue
0
gravatar for km
5.1 years ago by
km100
km100 wrote:
Hi all, I am unable to install Rgraphviz as a dependency for gage package. I am using R (3.0.2) and bioconductor 2.13. > biocLite('Rgraphviz') BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'Rgraphviz' trying URL ' http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2.6.0 .tar.gz ' Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) opened URL ... ... gcc -std=gnu99 -shared -L/usr/local/lib64 -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 gcc: error: libxdot.a: No such file or directory gcc: error: libgvplugin_dot_layout.a: No such file or directory gcc: error: libgvplugin_neato_layout.a: No such file or directory gcc: error: libgvplugin_core.a: No such file or directory gcc: error: libgvc.a: No such file or directory gcc: error: libpathplan.a: No such file or directory gcc: error: libgraph.a: No such file or directory gcc: error: libcdt.a: No such file or directory make: *** [Rgraphviz.so] Error 1 ERROR: compilation failed for package ‘Rgraphviz’ * removing ‘/home/km/lib64/R/library/Rgraphviz’ The downloaded source packages are in ‘/tmp/RtmpOFdCuI/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘Rgraphviz’ had non-zero exit status > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Regards, Krishna [[alternative HTML version deleted]]
rgraphviz gage • 877 views
ADD COMMENTlink modified 5.1 years ago by Luo Weijun1.4k • written 5.1 years ago by km100
Answer: Rgraphviz installation issue
0
gravatar for km
5.1 years ago by
km100
km100 wrote:
I am using gcc 4.7.3 on ubuntu Linux 13.04 ( x86_64 arch). Here is the complete trace: R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) 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. Natural language support but running in an English locale 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. [Previously saved workspace restored] > source('http://bioconductor.org/biocLite.R') Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite('Rgraphviz') BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.1. Installing package(s) 'Rgraphviz' trying URL ' http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2.6.0 .tar.gz ' Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) opened URL ================================================== downloaded 7.1 Mb * installing *source* package ‘Rgraphviz’ ... configure: Using bundled Graphviz. configure: Searching for the compilers specified by R. checking for gcc... gcc -std=gnu99 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=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes configure: Preparing to compile Graphviz. configure: Configuring bundled Graphviz. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /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=gnu99 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=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking dependency style of gcc -std=gnu99... 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... /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... no checking for tclsh8.5... /usr/bin/tclsh8.5 checking whether gcc -std=gnu99 and cc understand -c and -o together... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU Objective C compiler... no checking whether gcc accepts -g... no 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 -std=gnu99 -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... /bin/sed checking for fgrep... grep -F checking for ld used by gcc -std=gnu99... /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=gnu99 object... ok checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 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... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for ld used by g++... /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++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ 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/i386-linux-gnu/mesa /lib/i386-linux-gnu /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 /usr/lib32 /libx32 /usr/libx32 /home/km/lib checking for library containing dlopen... -ldl checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for 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... no checking for strlcpy... no checking for X... disabled configure: WARNING: X11 not available. checking tcl.h usability... no checking tcl.h presence... no checking for tcl.h... no configure: WARNING: Unable to find header tcl.h. The Tcl packages will not be built configure: WARNING: No Tcl. The Tk packages will not be built either checking for connect... yes checking for gethostbyname... yes checking for main in -lXpm... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for X11/Xaw/Text.h... yes checking for main in -lXaw... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for main in -lz... yes checking for deflateBound... no checking for GDK_PIXBUF... no checking for GTK... no 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... qmake checking for QTCORE... 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... yes 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 (/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix' 'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' 'LDFLAGS=-L/usr/local/lib' '-- libdir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib' '--includedir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/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' 'R_LIBS=/home/km/lib/R/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... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for style of include used by make... GNU checking for gcc... gcc -std=gnu99 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=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking dependency style of gcc -std=gnu99... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /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=gnu99 object... ok checking how to run the C preprocessor... gcc -std=gnu99 -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=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 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... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking which extension is used for runtime loadable modules... .so checking which variable specifies run-time module search path... LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/i386-linux-gnu/mesa /lib/i386-linux-gnu /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 /usr/lib32 /libx32 /usr/libx32 /home/km/lib checking for library containing dlopen... -ldl checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for unistd.h... (cached) yes checking for dl.h... no checking for sys/dl.h... no checking for dld.h... no checking for mach-o/dyld.h... no checking for dirent.h... yes checking for closedir... yes checking for opendir... yes checking for readdir... yes checking for strlcat... no checking for strlcpy... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands ---------------------------------------------------------------- graphviz-2.28.0 will be compiled with the following: options: cgraph: No (disabled by default - experimental) digcola: Yes expat: No (disabled) fontconfig: No (disabled) freetype: No (disabled) glut: No (disabled) gts: No (disabled) ipsepcola: No (disabled by default - C++ portability issues) ltdl: No (disabled) ortho: Yes png: No (disabled) jpeg: No (disabled) sfdp: Yes shared: No (disabled) static: Yes qt: No (QtCore not available) 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 (QtCore not available) 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: No (gdk_pixbuf library not available) ghostscript: No (disabled) glitz: No (disabled by default - incomplete) gtk: No (gtk library not available) lasi: No (disabled) ming: No (disabled by default - incomplete) pangocairo: No (disabled) quartz: No (disabled by default - Mac only) rsvg: No (disabled) visio: No (disabled by default - experimental) xlib: No (disabled or unavailable) language extensions: gv_sharp: No (swig not available) gv_go: No (disabled by default - experimental) gv_guile: No (swig not available) gv_io: No (disabled by default - no swig support yet) gv_java: No (swig not available) gv_lua: No (swig not available) gv_ocaml: No (swig not available) gv_perl: No (swig not available) gv_php: No (swig not available) gv_python: No (swig not available) gv_python23: No (disabled by default - for multiversion installs) gv_python24: No (disabled by default - for multiversion installs) gv_python25: No (disabled by default - for multiversion installs) gv_python26: No (disabled by default - for multiversion installs) gv_python27: No (disabled by default - for multiversion installs) gv_R: No (swig not available) gv_ruby: No (swig not available) gv_tcl: No (tcl not available) tcldot: No (tcl not available) tclpathplan: No (tcl not available) gdtclft: No (tcl not available) tkspline: No (tk not available) grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h make install-recursive make[1]: Entering directory `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' Making install in libltdl make[2]: Entering directory `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' make install-am make[3]: Entering directory `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' /bin/bash ./libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -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 -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fPIC -DPIC -o dlopen.o In file included from libltdl/lt__private.h:52:0, from loaders/dlopen.c:32: libltdl/lt__dirent.h:84:7: error: expected '=', ',', ';', 'asm' or '__attribute__' before '-' token make[3]: *** [dlopen.lo] Error 1 make[3]: Leaving directory `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' make[2]: *** [install] Error 2 make[2]: Leaving directory `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' make: *** [install] Error 2 cp: cannot stat '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/*': No such file or directory cp: cannot stat '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/graphviz /*': No such file or directory checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/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 zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for deflateBound in -lz... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for whether compiler has bool... yes configure: Using the following compilation and linking flags for Rgraphviz configure: PKG_CFLAGS= -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz 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 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 gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -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 gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c agopen.c -o agopen.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c agread.c -o agread.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c agwrite.c -o agwrite.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c bezier.c -o bezier.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c doLayout.c -o doLayout.o gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o graphvizVersion.c: In function ‘Rgraphviz_capabilities’: graphvizVersion.c:19:5: warning: implicit declaration of function ‘gvPluginList’ [-Wimplicit-function-declaration] graphvizVersion.c:19:8: warning: assignment makes pointer from integer without a cast [enabled by default] graphvizVersion.c:28:8: warning: assignment makes pointer from integer without a cast [enabled by default] graphvizVersion.c:37:8: warning: assignment makes pointer from integer without a cast [enabled by default] graphvizVersion.c:46:8: warning: assignment makes pointer from integer without a cast [enabled by default] graphvizVersion.c:55:8: warning: assignment makes pointer from integer without a cast [enabled by default] gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/gra phviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -shared -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 gcc: error: libxdot.a: No such file or directory gcc: error: libgvplugin_dot_layout.a: No such file or directory gcc: error: libgvplugin_neato_layout.a: No such file or directory gcc: error: libgvplugin_core.a: No such file or directory gcc: error: libgvc.a: No such file or directory gcc: error: libpathplan.a: No such file or directory gcc: error: libgraph.a: No such file or directory gcc: error: libcdt.a: No such file or directory make: *** [Rgraphviz.so] Error 1 ERROR: compilation failed for package ‘Rgraphviz’ * removing ‘/home/km/lib/R/library/Rgraphviz’ The downloaded source packages are in ‘/tmp/RtmpPVdgYk/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Old packages: 'snowfall' Update all/some/none? [a/s/n]: n Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘Rgraphviz’ had non-zero exit status > Regards, Krishna On Thu, Dec 19, 2013 at 8:52 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > We want the full output from the installation, despite its length. Also, > which version of gcc are you using? > > Best, > Kaspe > > > On Thu, Dec 19, 2013 at 11:28 AM, km <srikrishnamohan@gmail.com> wrote: > >> Hi all, >> >> I am unable to install Rgraphviz as a dependency for gage package. >> I am using R (3.0.2) and bioconductor 2.13. >> >> > >> biocLite('Rgraphviz') >> >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. >> Installing package(s) 'Rgraphviz' >> trying URL ' >> >> http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2. 6.0.tar.gz >> ' >> Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) >> opened URL >> ... >> ... >> gcc -std=gnu99 -shared -L/usr/local/lib64 -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 >> gcc: error: libxdot.a: No such file or directory >> gcc: error: libgvplugin_dot_layout.a: No such file or directory >> gcc: error: libgvplugin_neato_layout.a: No such file or directory >> gcc: error: libgvplugin_core.a: No such file or directory >> gcc: error: libgvc.a: No such file or directory >> gcc: error: libpathplan.a: No such file or directory >> gcc: error: libgraph.a: No such file or directory >> gcc: error: libcdt.a: No such file or directory >> make: *** [Rgraphviz.so] Error 1 >> ERROR: compilation failed for package ‘Rgraphviz’ >> * removing ‘/home/km/lib64/R/library/Rgraphviz’ >> >> The downloaded source packages are in >> ‘/tmp/RtmpOFdCuI/downloaded_packages’ >> Updating HTML index of packages in '.Library' >> Making 'packages.html' ... done >> Warning message: >> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ‘Rgraphviz’ had non-zero exit status >> >> >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> Regards, >> Krishna >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.1 years ago by km100
Thanks, this might be hard to fix, but I will try to have a look at it. Xmas is not going to make this go faster. The issue is with compiling libltdl, I am surprised we have not seen this earlier; looks like something where GCC 4.7 have gotten strict(er), but I am pretty sure people have build with GCC 4.7 before. Kasper On Fri, Dec 20, 2013 at 4:59 AM, km <srikrishnamohan@gmail.com> wrote: > I am using gcc 4.7.3 on ubuntu Linux 13.04 ( x86_64 arch). > > Here is the complete trace: > > R version 3.0.1 (2013-05-16) -- "Good Sport" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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. > > Natural language support but running in an English locale > > 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. > > [Previously saved workspace restored] > > source('http://bioconductor.org/biocLite.R') > Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > > > > biocLite('Rgraphviz') > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.1. > > Installing package(s) 'Rgraphviz' > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2.6 .0.tar.gz > ' > Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) > opened URL > ================================================== > downloaded 7.1 Mb > > * installing *source* package ‘Rgraphviz’ ... > configure: Using bundled Graphviz. > configure: Searching for the compilers specified by R. > checking for gcc... gcc -std=gnu99 > 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=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking whether we are using the GNU C++ compiler... yes > checking whether g++ accepts -g... yes > configure: Preparing to compile Graphviz. > configure: Configuring bundled Graphviz. > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... /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=gnu99 > 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=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking dependency style of gcc -std=gnu99... 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... /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... no > checking for tclsh8.5... /usr/bin/tclsh8.5 > checking whether gcc -std=gnu99 and cc understand -c and -o together... yes > checking whether we are using the GNU C++ compiler... yes > checking whether g++ accepts -g... yes > checking dependency style of g++... gcc3 > checking for gcc... gcc > checking whether we are using the GNU Objective C compiler... no > checking whether gcc accepts -g... no > 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 -std=gnu99 -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... /bin/sed > checking for fgrep... grep -F > checking for ld used by gcc -std=gnu99... /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=gnu99 > object... ok > checking for dlfcn.h... yes > checking whether we are using the GNU C++ compiler... (cached) yes > checking whether g++ accepts -g... (cached) yes > checking dependency style of g++... (cached) gcc3 > checking how to run the C++ preprocessor... g++ -E > checking for objdir... .libs > checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no > checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC > checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes > checking if gcc -std=gnu99 static flag -static works... yes > checking if gcc -std=gnu99 supports -c -o file.o... yes > checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes > checking whether the gcc -std=gnu99 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... no > checking for dlopen in -ldl... yes > checking whether a program can dlopen itself... yes > checking whether a statically linked program can dlopen itself... no > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... no > checking whether to build static libraries... yes > checking for ld used by g++... /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++ linker (/usr/bin/ld -m elf_x86_64) supports > shared libraries... yes > checking for g++ option to produce PIC... -fPIC -DPIC > checking if g++ PIC flag -fPIC -DPIC works... yes > checking if g++ static flag -static works... yes > checking if g++ supports -c -o file.o... yes > checking if g++ supports -c -o file.o... (cached) yes > checking whether the g++ 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/i386-linux-gnu/mesa /lib/i386-linux-gnu > /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu > /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu > /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 > /usr/lib32 /libx32 /usr/libx32 /home/km/lib > checking for library containing dlopen... -ldl > checking for dlerror... yes > checking for shl_load... (cached) no > checking for shl_load in -ldld... (cached) no > checking for dld_link in -ldld... no > checking for _ prefix in compiled symbols... no > checking whether deplibs are loaded by dlopen... yes > checking for argz.h... yes > checking for error_t... yes > checking for argz_add... yes > checking for argz_append... yes > checking for argz_count... yes > checking for argz_create_sep... yes > checking for argz_insert... yes > checking for argz_next... yes > checking for argz_stringify... yes > checking if argz actually works... yes > checking whether libtool supports -dlopen/-dlpreopen... yes > checking for 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... no > checking for strlcpy... no > checking for X... disabled > configure: WARNING: X11 not available. > checking tcl.h usability... no > checking tcl.h presence... no > checking for tcl.h... no > configure: WARNING: Unable to find header tcl.h. The Tcl packages will not > be built > configure: WARNING: No Tcl. The Tk packages will not be built either > checking for connect... yes > checking for gethostbyname... yes > checking for main in -lXpm... yes > checking X11/Intrinsic.h usability... yes > checking X11/Intrinsic.h presence... yes > checking for X11/Intrinsic.h... yes > checking for X11/Xaw/Text.h... yes > checking for main in -lXaw... yes > checking zlib.h usability... yes > checking zlib.h presence... yes > checking for zlib.h... yes > checking for main in -lz... yes > checking for deflateBound... no > checking for GDK_PIXBUF... no > checking for GTK... no > 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... qmake > checking for QTCORE... 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... yes > 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 > (/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl) > configure: running /bin/bash ./configure --disable-option-checking > '--prefix=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix' > 'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' > 'LDFLAGS=-L/usr/local/lib' > '-- libdir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib' > '--includedir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libun ix/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' > 'R_LIBS=/home/km/lib/R/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... /bin/mkdir -p > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking for style of include used by make... GNU > checking for gcc... gcc -std=gnu99 > 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=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking dependency style of gcc -std=gnu99... gcc3 > checking for a sed that does not truncate output... /bin/sed > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for fgrep... /bin/grep -F > checking for ld used by gcc -std=gnu99... /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=gnu99 > object... ok > checking how to run the C preprocessor... gcc -std=gnu99 -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=gnu99 supports -fno-rtti -fno-exceptions... no > checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC > checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes > checking if gcc -std=gnu99 static flag -static works... yes > checking if gcc -std=gnu99 supports -c -o file.o... yes > checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes > checking whether the gcc -std=gnu99 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... no > checking for dlopen in -ldl... yes > checking whether a program can dlopen itself... yes > checking whether a statically linked program can dlopen itself... no > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... no > checking whether to build static libraries... yes > checking which extension is used for runtime loadable modules... .so > checking which variable specifies run-time module search path... > LD_LIBRARY_PATH > checking for the default library search path... /lib64 /usr/lib64 /lib > /usr/lib /usr/lib/i386-linux-gnu/mesa /lib/i386-linux-gnu > /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu > /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu > /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 > /usr/lib32 /libx32 /usr/libx32 /home/km/lib > checking for library containing dlopen... -ldl > checking for dlerror... yes > checking for shl_load... (cached) no > checking for shl_load in -ldld... (cached) no > checking for dld_link in -ldld... no > checking for _ prefix in compiled symbols... no > checking whether deplibs are loaded by dlopen... yes > checking for argz.h... yes > checking for error_t... yes > checking for argz_add... yes > checking for argz_append... yes > checking for argz_count... yes > checking for argz_create_sep... yes > checking for argz_insert... yes > checking for argz_next... yes > checking for argz_stringify... yes > checking if argz actually works... yes > checking whether libtool supports -dlopen/-dlpreopen... yes > checking for unistd.h... (cached) yes > checking for dl.h... no > checking for sys/dl.h... no > checking for dld.h... no > checking for mach-o/dyld.h... no > checking for dirent.h... yes > checking for closedir... yes > checking for opendir... yes > checking for readdir... yes > checking for strlcat... no > checking for strlcpy... no > checking that generated files are newer than configure... done > configure: creating ./config.status > config.status: creating Makefile > config.status: creating config.h > config.status: executing depfiles commands > config.status: executing libtool commands > > ---------------------------------------------------------------- > > graphviz-2.28.0 will be compiled with the following: > > options: > cgraph: No (disabled by default - experimental) > digcola: Yes > expat: No (disabled) > fontconfig: No (disabled) > freetype: No (disabled) > glut: No (disabled) > gts: No (disabled) > ipsepcola: No (disabled by default - C++ portability issues) > ltdl: No (disabled) > ortho: Yes > png: No (disabled) > jpeg: No (disabled) > sfdp: Yes > shared: No (disabled) > static: Yes > qt: No (QtCore not available) > > 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 (QtCore not available) > > 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: No (gdk_pixbuf library not available) > ghostscript: No (disabled) > glitz: No (disabled by default - incomplete) > gtk: No (gtk library not available) > lasi: No (disabled) > ming: No (disabled by default - incomplete) > pangocairo: No (disabled) > quartz: No (disabled by default - Mac only) > rsvg: No (disabled) > visio: No (disabled by default - experimental) > xlib: No (disabled or unavailable) > > language extensions: > gv_sharp: No (swig not available) > gv_go: No (disabled by default - experimental) > gv_guile: No (swig not available) > gv_io: No (disabled by default - no swig support yet) > gv_java: No (swig not available) > gv_lua: No (swig not available) > gv_ocaml: No (swig not available) > gv_perl: No (swig not available) > gv_php: No (swig not available) > gv_python: No (swig not available) > gv_python23: No (disabled by default - for multiversion installs) > gv_python24: No (disabled by default - for multiversion installs) > gv_python25: No (disabled by default - for multiversion installs) > gv_python26: No (disabled by default - for multiversion installs) > gv_python27: No (disabled by default - for multiversion installs) > gv_R: No (swig not available) > gv_ruby: No (swig not available) > gv_tcl: No (tcl not available) > > tcldot: No (tcl not available) > tclpathplan: No (tcl not available) > gdtclft: No (tcl not available) > tkspline: No (tk not available) > grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h > make install-recursive > make[1]: Entering directory > `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' > Making install in libltdl > make[2]: Entering directory > `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' > make install-am > make[3]: Entering directory > `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' > /bin/bash ./libtool --tag=CC --mode=compile gcc -std=gnu99 > -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl > -I./libltdl -I./libltdl -g -O2 -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 -std=gnu99 -DHAVE_CONFIG_H -I. > "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl > -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c > -fPIC -DPIC -o dlopen.o > In file included from libltdl/lt__private.h:52:0, > from loaders/dlopen.c:32: > libltdl/lt__dirent.h:84:7: error: expected '=', ',', ';', 'asm' or > '__attribute__' before '-' token > make[3]: *** [dlopen.lo] Error 1 > make[3]: Leaving directory > `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' > make[2]: *** [install] Error 2 > make[2]: Leaving directory > `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory > `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' > make: *** [install] Error 2 > cp: cannot stat > '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/*': No such > file or directory > cp: cannot stat > '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/graphv iz/*': > No such file or directory > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/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 zlib.h usability... yes > checking zlib.h presence... yes > checking for zlib.h... yes > checking for deflateBound in -lz... yes > checking for stdbool.h that conforms to C99... yes > checking for _Bool... yes > checking for whether compiler has bool... yes > configure: Using the following compilation and linking flags for Rgraphviz > configure: PKG_CFLAGS= > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > 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 > 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 > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -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 > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c agopen.c -o agopen.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c agread.c -o agread.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c agwrite.c -o agwrite.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c bezier.c -o bezier.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c doLayout.c -o doLayout.o > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o > graphvizVersion.c: In function ‘Rgraphviz_capabilities’: > graphvizVersion.c:19:5: warning: implicit declaration of function > ‘gvPluginList’ [-Wimplicit-function-declaration] > graphvizVersion.c:19:8: warning: assignment makes pointer from integer > without a cast [enabled by default] > graphvizVersion.c:28:8: warning: assignment makes pointer from integer > without a cast [enabled by default] > graphvizVersion.c:37:8: warning: assignment makes pointer from integer > without a cast [enabled by default] > graphvizVersion.c:46:8: warning: assignment makes pointer from integer > without a cast [enabled by default] > graphvizVersion.c:55:8: warning: assignment makes pointer from integer > without a cast [enabled by default] > gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include > -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/g raphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 > -DHAVE_BOOL=1 -fpic -g -O2 -c init.c -o init.o > gcc -std=gnu99 -shared -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 > > gcc: error: libxdot.a: No such file or directory > gcc: error: libgvplugin_dot_layout.a: No such file or directory > gcc: error: libgvplugin_neato_layout.a: No such file or directory > gcc: error: libgvplugin_core.a: No such file or directory > gcc: error: libgvc.a: No such file or directory > gcc: error: libpathplan.a: No such file or directory > gcc: error: libgraph.a: No such file or directory > gcc: error: libcdt.a: No such file or directory > make: *** [Rgraphviz.so] Error 1 > ERROR: compilation failed for package ‘Rgraphviz’ > * removing ‘/home/km/lib/R/library/Rgraphviz’ > > > The downloaded source packages are in > ‘/tmp/RtmpPVdgYk/downloaded_packages’ > > Updating HTML index of packages in '.Library' > Making 'packages.html' ... done > Old packages: 'snowfall' > Update all/some/none? [a/s/n]: n > > Warning message: > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘Rgraphviz’ had non-zero exit status > > > > Regards, > Krishna > > > On Thu, Dec 19, 2013 at 8:52 PM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com> wrote: > >> We want the full output from the installation, despite its length. Also, >> which version of gcc are you using? >> >> Best, >> Kaspe >> >> >> On Thu, Dec 19, 2013 at 11:28 AM, km <srikrishnamohan@gmail.com> wrote: >> >>> Hi all, >>> >>> I am unable to install Rgraphviz as a dependency for gage package. >>> I am using R (3.0.2) and bioconductor 2.13. >>> >>> > >>> biocLite('Rgraphviz') >>> >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. >>> Installing package(s) 'Rgraphviz' >>> trying URL ' >>> >>> http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2 .6.0.tar.gz >>> ' >>> Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) >>> opened URL >>> ... >>> ... >>> gcc -std=gnu99 -shared -L/usr/local/lib64 -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 >>> gcc: error: libxdot.a: No such file or directory >>> gcc: error: libgvplugin_dot_layout.a: No such file or directory >>> gcc: error: libgvplugin_neato_layout.a: No such file or directory >>> gcc: error: libgvplugin_core.a: No such file or directory >>> gcc: error: libgvc.a: No such file or directory >>> gcc: error: libpathplan.a: No such file or directory >>> gcc: error: libgraph.a: No such file or directory >>> gcc: error: libcdt.a: No such file or directory >>> make: *** [Rgraphviz.so] Error 1 >>> ERROR: compilation failed for package ‘Rgraphviz’ >>> * removing ‘/home/km/lib64/R/library/Rgraphviz’ >>> >>> The downloaded source packages are in >>> ‘/tmp/RtmpOFdCuI/downloaded_packages’ >>> Updating HTML index of packages in '.Library' >>> Making 'packages.html' ... done >>> Warning message: >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>> installation of package ‘Rgraphviz’ had non-zero exit status >>> >>> >>> >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> Regards, >>> Krishna >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
ADD REPLYlink written 5.1 years ago by Kasper Daniel Hansen6.4k
Some follow up. I have exchanged some private emails with Kipper Fletez-Brant (cc'ed) on this issue. He uses almost the exact same system as Krishna, i.e.. "R 3.0.1, Ubuntu 13.04 and gcc 4.7.3". The R version is slightly different but I cannot fathom why that should matter with this issue. It works for Kipper. Comparing the installation output, his line for compiling the dlopen.c file is libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -O2 -pipe -g -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fPIC -DPIC -o dlopen.o whereas Krishna has libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fPIC -DPIC -o dlopen.o (no -pipe). Furthermore, I am suspicious of the following difference reported by configure where Kipper has checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux- gnu /usr/lib/x86_64-linux-gnu/mesa Krishna has checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib/i386-linux-gnu/mesa /lib/i386-linux-gnu /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 /usr/lib32 /libx32 /usr/libx32 /home/km/lib This is a peculiar mix of something that looks like 32bit and 64 bit system libraries. Sure this is correct? Have you set LIBRARY_PATH or LD_LIBRARY_PATH, if so, how? Best, Kasper On Fri, Dec 20, 2013 at 11:42 AM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Thanks, this might be hard to fix, but I will try to have a look at it. > Xmas is not going to make this go faster. The issue is with compiling > libltdl, I am surprised we have not seen this earlier; looks like something > where GCC 4.7 have gotten strict(er), but I am pretty sure people have > build with GCC 4.7 before. > > Kasper > > > On Fri, Dec 20, 2013 at 4:59 AM, km <srikrishnamohan@gmail.com> wrote: > >> I am using gcc 4.7.3 on ubuntu Linux 13.04 ( x86_64 arch). >> >> Here is the complete trace: >> >> R version 3.0.1 (2013-05-16) -- "Good Sport" >> Copyright (C) 2013 The R Foundation for Statistical Computing >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> 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. >> >> Natural language support but running in an English locale >> >> 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. >> >> [Previously saved workspace restored] >> > source('http://bioconductor.org/biocLite.R') >> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >> >> >> > biocLite('Rgraphviz') >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.1. >> >> Installing package(s) 'Rgraphviz' >> trying URL ' >> http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2. 6.0.tar.gz >> ' >> Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) >> opened URL >> ================================================== >> downloaded 7.1 Mb >> >> * installing *source* package ‘Rgraphviz’ ... >> configure: Using bundled Graphviz. >> configure: Searching for the compilers specified by R. >> checking for gcc... gcc -std=gnu99 >> 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=gnu99 accepts -g... yes >> checking for gcc -std=gnu99 option to accept ISO C89... none needed >> checking how to run the C preprocessor... gcc -std=gnu99 -E >> checking whether we are using the GNU C++ compiler... yes >> checking whether g++ accepts -g... yes >> configure: Preparing to compile Graphviz. >> configure: Configuring bundled Graphviz. >> checking build system type... x86_64-unknown-linux-gnu >> checking host system type... x86_64-unknown-linux-gnu >> checking for a BSD-compatible install... /usr/bin/install -c >> checking whether build environment is sane... yes >> checking for a thread-safe mkdir -p... /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=gnu99 >> 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=gnu99 accepts -g... yes >> checking for gcc -std=gnu99 option to accept ISO C89... none needed >> checking dependency style of gcc -std=gnu99... 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... /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... no >> checking for tclsh8.5... /usr/bin/tclsh8.5 >> checking whether gcc -std=gnu99 and cc understand -c and -o together... >> yes >> checking whether we are using the GNU C++ compiler... yes >> checking whether g++ accepts -g... yes >> checking dependency style of g++... gcc3 >> checking for gcc... gcc >> checking whether we are using the GNU Objective C compiler... no >> checking whether gcc accepts -g... no >> 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 -std=gnu99 -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... /bin/sed >> checking for fgrep... grep -F >> checking for ld used by gcc -std=gnu99... /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=gnu99 >> object... ok >> checking for dlfcn.h... yes >> checking whether we are using the GNU C++ compiler... (cached) yes >> checking whether g++ accepts -g... (cached) yes >> checking dependency style of g++... (cached) gcc3 >> checking how to run the C++ preprocessor... g++ -E >> checking for objdir... .libs >> checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no >> checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC >> checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes >> checking if gcc -std=gnu99 static flag -static works... yes >> checking if gcc -std=gnu99 supports -c -o file.o... yes >> checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes >> checking whether the gcc -std=gnu99 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... no >> checking for dlopen in -ldl... yes >> checking whether a program can dlopen itself... yes >> checking whether a statically linked program can dlopen itself... no >> checking whether stripping libraries is possible... yes >> checking if libtool supports shared libraries... yes >> checking whether to build shared libraries... no >> checking whether to build static libraries... yes >> checking for ld used by g++... /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++ linker (/usr/bin/ld -m elf_x86_64) supports >> shared libraries... yes >> checking for g++ option to produce PIC... -fPIC -DPIC >> checking if g++ PIC flag -fPIC -DPIC works... yes >> checking if g++ static flag -static works... yes >> checking if g++ supports -c -o file.o... yes >> checking if g++ supports -c -o file.o... (cached) yes >> checking whether the g++ 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/i386-linux-gnu/mesa /lib/i386-linux-gnu >> /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu >> /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu >> /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 >> /usr/lib32 /libx32 /usr/libx32 /home/km/lib >> checking for library containing dlopen... -ldl >> checking for dlerror... yes >> checking for shl_load... (cached) no >> checking for shl_load in -ldld... (cached) no >> checking for dld_link in -ldld... no >> checking for _ prefix in compiled symbols... no >> checking whether deplibs are loaded by dlopen... yes >> checking for argz.h... yes >> checking for error_t... yes >> checking for argz_add... yes >> checking for argz_append... yes >> checking for argz_count... yes >> checking for argz_create_sep... yes >> checking for argz_insert... yes >> checking for argz_next... yes >> checking for argz_stringify... yes >> checking if argz actually works... yes >> checking whether libtool supports -dlopen/-dlpreopen... yes >> checking for 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... no >> checking for strlcpy... no >> checking for X... disabled >> configure: WARNING: X11 not available. >> checking tcl.h usability... no >> checking tcl.h presence... no >> checking for tcl.h... no >> configure: WARNING: Unable to find header tcl.h. The Tcl packages will >> not be built >> configure: WARNING: No Tcl. The Tk packages will not be built either >> checking for connect... yes >> checking for gethostbyname... yes >> checking for main in -lXpm... yes >> checking X11/Intrinsic.h usability... yes >> checking X11/Intrinsic.h presence... yes >> checking for X11/Intrinsic.h... yes >> checking for X11/Xaw/Text.h... yes >> checking for main in -lXaw... yes >> checking zlib.h usability... yes >> checking zlib.h presence... yes >> checking for zlib.h... yes >> checking for main in -lz... yes >> checking for deflateBound... no >> checking for GDK_PIXBUF... no >> checking for GTK... no >> 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... qmake >> checking for QTCORE... 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... yes >> 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 >> (/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl) >> configure: running /bin/bash ./configure --disable-option-checking >> '--prefix=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix' >> 'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' >> 'LDFLAGS=-L/usr/local/lib' >> '-- libdir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib' >> '--includedir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libu nix/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' >> 'R_LIBS=/home/km/lib/R/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... /bin/mkdir -p >> checking for gawk... gawk >> checking whether make sets $(MAKE)... yes >> checking build system type... x86_64-unknown-linux-gnu >> checking host system type... x86_64-unknown-linux-gnu >> checking for style of include used by make... GNU >> checking for gcc... gcc -std=gnu99 >> 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=gnu99 accepts -g... yes >> checking for gcc -std=gnu99 option to accept ISO C89... none needed >> checking dependency style of gcc -std=gnu99... gcc3 >> checking for a sed that does not truncate output... /bin/sed >> checking for grep that handles long lines and -e... /bin/grep >> checking for egrep... /bin/grep -E >> checking for fgrep... /bin/grep -F >> checking for ld used by gcc -std=gnu99... /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=gnu99 >> object... ok >> checking how to run the C preprocessor... gcc -std=gnu99 -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=gnu99 supports -fno-rtti -fno-exceptions... no >> checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC >> checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes >> checking if gcc -std=gnu99 static flag -static works... yes >> checking if gcc -std=gnu99 supports -c -o file.o... yes >> checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes >> checking whether the gcc -std=gnu99 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... no >> checking for dlopen in -ldl... yes >> checking whether a program can dlopen itself... yes >> checking whether a statically linked program can dlopen itself... no >> checking whether stripping libraries is possible... yes >> checking if libtool supports shared libraries... yes >> checking whether to build shared libraries... no >> checking whether to build static libraries... yes >> checking which extension is used for runtime loadable modules... .so >> checking which variable specifies run-time module search path... >> LD_LIBRARY_PATH >> checking for the default library search path... /lib64 /usr/lib64 /lib >> /usr/lib /usr/lib/i386-linux-gnu/mesa /lib/i386-linux-gnu >> /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu >> /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu >> /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 >> /usr/lib32 /libx32 /usr/libx32 /home/km/lib >> checking for library containing dlopen... -ldl >> checking for dlerror... yes >> checking for shl_load... (cached) no >> checking for shl_load in -ldld... (cached) no >> checking for dld_link in -ldld... no >> checking for _ prefix in compiled symbols... no >> checking whether deplibs are loaded by dlopen... yes >> checking for argz.h... yes >> checking for error_t... yes >> checking for argz_add... yes >> checking for argz_append... yes >> checking for argz_count... yes >> checking for argz_create_sep... yes >> checking for argz_insert... yes >> checking for argz_next... yes >> checking for argz_stringify... yes >> checking if argz actually works... yes >> checking whether libtool supports -dlopen/-dlpreopen... yes >> checking for unistd.h... (cached) yes >> checking for dl.h... no >> checking for sys/dl.h... no >> checking for dld.h... no >> checking for mach-o/dyld.h... no >> checking for dirent.h... yes >> checking for closedir... yes >> checking for opendir... yes >> checking for readdir... yes >> checking for strlcat... no >> checking for strlcpy... no >> checking that generated files are newer than configure... done >> configure: creating ./config.status >> config.status: creating Makefile >> config.status: creating config.h >> config.status: executing depfiles commands >> config.status: executing libtool commands >> >> ---------------------------------------------------------------- >> >> graphviz-2.28.0 will be compiled with the following: >> >> options: >> cgraph: No (disabled by default - experimental) >> digcola: Yes >> expat: No (disabled) >> fontconfig: No (disabled) >> freetype: No (disabled) >> glut: No (disabled) >> gts: No (disabled) >> ipsepcola: No (disabled by default - C++ portability issues) >> ltdl: No (disabled) >> ortho: Yes >> png: No (disabled) >> jpeg: No (disabled) >> sfdp: Yes >> shared: No (disabled) >> static: Yes >> qt: No (QtCore not available) >> >> 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 (QtCore not available) >> >> 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: No (gdk_pixbuf library not available) >> ghostscript: No (disabled) >> glitz: No (disabled by default - incomplete) >> gtk: No (gtk library not available) >> lasi: No (disabled) >> ming: No (disabled by default - incomplete) >> pangocairo: No (disabled) >> quartz: No (disabled by default - Mac only) >> rsvg: No (disabled) >> visio: No (disabled by default - experimental) >> xlib: No (disabled or unavailable) >> >> language extensions: >> gv_sharp: No (swig not available) >> gv_go: No (disabled by default - experimental) >> gv_guile: No (swig not available) >> gv_io: No (disabled by default - no swig support yet) >> gv_java: No (swig not available) >> gv_lua: No (swig not available) >> gv_ocaml: No (swig not available) >> gv_perl: No (swig not available) >> gv_php: No (swig not available) >> gv_python: No (swig not available) >> gv_python23: No (disabled by default - for multiversion installs) >> gv_python24: No (disabled by default - for multiversion installs) >> gv_python25: No (disabled by default - for multiversion installs) >> gv_python26: No (disabled by default - for multiversion installs) >> gv_python27: No (disabled by default - for multiversion installs) >> gv_R: No (swig not available) >> gv_ruby: No (swig not available) >> gv_tcl: No (tcl not available) >> >> tcldot: No (tcl not available) >> tclpathplan: No (tcl not available) >> gdtclft: No (tcl not available) >> tkspline: No (tk not available) >> grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h >> make install-recursive >> make[1]: Entering directory >> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' >> Making install in libltdl >> make[2]: Entering directory >> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >> make install-am >> make[3]: Entering directory >> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >> /bin/bash ./libtool --tag=CC --mode=compile gcc -std=gnu99 >> -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl >> -I./libltdl -I./libltdl -g -O2 -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 -std=gnu99 -DHAVE_CONFIG_H -I. >> "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl >> -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c >> -fPIC -DPIC -o dlopen.o >> In file included from libltdl/lt__private.h:52:0, >> from loaders/dlopen.c:32: >> libltdl/lt__dirent.h:84:7: error: expected '=', ',', ';', 'asm' or >> '__attribute__' before '-' token >> make[3]: *** [dlopen.lo] Error 1 >> make[3]: Leaving directory >> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >> make[2]: *** [install] Error 2 >> make[2]: Leaving directory >> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory >> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' >> make: *** [install] Error 2 >> cp: cannot stat >> '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/*': No such >> file or directory >> cp: cannot stat >> '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/graph viz/*': >> No such file or directory >> checking for grep that handles long lines and -e... /bin/grep >> checking for egrep... /bin/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 zlib.h usability... yes >> checking zlib.h presence... yes >> checking for zlib.h... yes >> checking for deflateBound in -lz... yes >> checking for stdbool.h that conforms to C99... yes >> checking for _Bool... yes >> checking for whether compiler has bool... yes >> configure: Using the following compilation and linking flags for Rgraphviz >> configure: PKG_CFLAGS= >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/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 >> 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 >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/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 >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c agopen.c -o agopen.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c agread.c -o agread.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c agwrite.c -o agwrite.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c bezier.c -o bezier.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c doLayout.c -o doLayout.o >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o >> graphvizVersion.c: In function ‘Rgraphviz_capabilities’: >> graphvizVersion.c:19:5: warning: implicit declaration of function >> ‘gvPluginList’ [-Wimplicit-function-declaration] >> graphvizVersion.c:19:8: warning: assignment makes pointer from integer >> without a cast [enabled by default] >> graphvizVersion.c:28:8: warning: assignment makes pointer from integer >> without a cast [enabled by default] >> graphvizVersion.c:37:8: warning: assignment makes pointer from integer >> without a cast [enabled by default] >> graphvizVersion.c:46:8: warning: assignment makes pointer from integer >> without a cast [enabled by default] >> graphvizVersion.c:55:8: warning: assignment makes pointer from integer >> without a cast [enabled by default] >> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include/ graphviz >> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >> -DHAVE_BOOL=1 -fpic -g -O2 -c init.c -o init.o >> gcc -std=gnu99 -shared -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 >> >> gcc: error: libxdot.a: No such file or directory >> gcc: error: libgvplugin_dot_layout.a: No such file or directory >> gcc: error: libgvplugin_neato_layout.a: No such file or directory >> gcc: error: libgvplugin_core.a: No such file or directory >> gcc: error: libgvc.a: No such file or directory >> gcc: error: libpathplan.a: No such file or directory >> gcc: error: libgraph.a: No such file or directory >> gcc: error: libcdt.a: No such file or directory >> make: *** [Rgraphviz.so] Error 1 >> ERROR: compilation failed for package ‘Rgraphviz’ >> * removing ‘/home/km/lib/R/library/Rgraphviz’ >> >> >> The downloaded source packages are in >> ‘/tmp/RtmpPVdgYk/downloaded_packages’ >> >> Updating HTML index of packages in '.Library' >> Making 'packages.html' ... done >> Old packages: 'snowfall' >> Update all/some/none? [a/s/n]: n >> >> Warning message: >> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ‘Rgraphviz’ had non-zero exit status >> > >> >> Regards, >> Krishna >> >> >> On Thu, Dec 19, 2013 at 8:52 PM, Kasper Daniel Hansen < >> kasperdanielhansen@gmail.com> wrote: >> >>> We want the full output from the installation, despite its length. Also, >>> which version of gcc are you using? >>> >>> Best, >>> Kaspe >>> >>> >>> On Thu, Dec 19, 2013 at 11:28 AM, km <srikrishnamohan@gmail.com> wrote: >>> >>>> Hi all, >>>> >>>> I am unable to install Rgraphviz as a dependency for gage package. >>>> I am using R (3.0.2) and bioconductor 2.13. >>>> >>>> > >>>> biocLite('Rgraphviz') >>>> >>>> BioC_mirror: http://bioconductor.org >>>> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. >>>> Installing package(s) 'Rgraphviz' >>>> trying URL ' >>>> >>>> http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_ 2.6.0.tar.gz >>>> ' >>>> Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) >>>> opened URL >>>> ... >>>> ... >>>> gcc -std=gnu99 -shared -L/usr/local/lib64 -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 >>>> gcc: error: libxdot.a: No such file or directory >>>> gcc: error: libgvplugin_dot_layout.a: No such file or directory >>>> gcc: error: libgvplugin_neato_layout.a: No such file or directory >>>> gcc: error: libgvplugin_core.a: No such file or directory >>>> gcc: error: libgvc.a: No such file or directory >>>> gcc: error: libpathplan.a: No such file or directory >>>> gcc: error: libgraph.a: No such file or directory >>>> gcc: error: libcdt.a: No such file or directory >>>> make: *** [Rgraphviz.so] Error 1 >>>> ERROR: compilation failed for package ‘Rgraphviz’ >>>> * removing ‘/home/km/lib64/R/library/Rgraphviz’ >>>> >>>> The downloaded source packages are in >>>> ‘/tmp/RtmpOFdCuI/downloaded_packages’ >>>> Updating HTML index of packages in '.Library' >>>> Making 'packages.html' ... done >>>> Warning message: >>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>>> installation of package ‘Rgraphviz’ had non-zero exit status >>>> >>>> >>>> >>>> > sessionInfo() >>>> R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> Regards, >>>> Krishna >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> > [[alternative HTML version deleted]]
ADD REPLYlink written 5.1 years ago by Kasper Daniel Hansen6.4k
Let me be more clear re. the issue with dealt library search path: it looks like Krishna may have a misconfigured system. How that manifest itself in this compilation issue, I don't know. Kasper On Tue, Dec 24, 2013 at 12:03 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Some follow up. I have exchanged some private emails with Kipper > Fletez-Brant (cc'ed) on this issue. He uses almost the exact same system > as Krishna, i.e.. "R 3.0.1, Ubuntu 13.04 and gcc 4.7.3". The R version > is slightly different but I cannot fathom why that should matter with this > issue. It works for Kipper. Comparing the installation output, his line > for compiling the dlopen.c file is > libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. > "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl > -O2 -pipe -g -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c > -fPIC -DPIC -o dlopen.o > whereas Krishna has > libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. > "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl > -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c > -fPIC -DPIC -o dlopen.o > > (no -pipe). Furthermore, I am suspicious of the following difference > reported by configure where Kipper has > checking for the default library search path... /lib64 /usr/lib64 /lib > /usr/lib /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux- gnu > /usr/lib/x86_64-linux-gnu/mesa > Krishna has > checking for the default library search path... /lib64 /usr/lib64 /lib > /usr/lib /usr/lib/i386-linux-gnu/mesa /lib/i386-linux-gnu > /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux-gnu > /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu > /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 > /usr/lib32 /libx32 /usr/libx32 /home/km/lib > > This is a peculiar mix of something that looks like 32bit and 64 bit > system libraries. Sure this is correct? Have you set LIBRARY_PATH or > LD_LIBRARY_PATH, if so, how? > > Best, > Kasper > > > > On Fri, Dec 20, 2013 at 11:42 AM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com> wrote: > >> Thanks, this might be hard to fix, but I will try to have a look at it. >> Xmas is not going to make this go faster. The issue is with compiling >> libltdl, I am surprised we have not seen this earlier; looks like something >> where GCC 4.7 have gotten strict(er), but I am pretty sure people have >> build with GCC 4.7 before. >> >> Kasper >> >> >> On Fri, Dec 20, 2013 at 4:59 AM, km <srikrishnamohan@gmail.com> wrote: >> >>> I am using gcc 4.7.3 on ubuntu Linux 13.04 ( x86_64 arch). >>> >>> Here is the complete trace: >>> >>> R version 3.0.1 (2013-05-16) -- "Good Sport" >>> Copyright (C) 2013 The R Foundation for Statistical Computing >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> 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. >>> >>> Natural language support but running in an English locale >>> >>> 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. >>> >>> [Previously saved workspace restored] >>> > source('http://bioconductor.org/biocLite.R') >>> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >>> >>> >>> > biocLite('Rgraphviz') >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.1. >>> >>> Installing package(s) 'Rgraphviz' >>> trying URL ' >>> http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2 .6.0.tar.gz >>> ' >>> Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) >>> opened URL >>> ================================================== >>> downloaded 7.1 Mb >>> >>> * installing *source* package ‘Rgraphviz’ ... >>> configure: Using bundled Graphviz. >>> configure: Searching for the compilers specified by R. >>> checking for gcc... gcc -std=gnu99 >>> 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=gnu99 accepts -g... yes >>> checking for gcc -std=gnu99 option to accept ISO C89... none needed >>> checking how to run the C preprocessor... gcc -std=gnu99 -E >>> checking whether we are using the GNU C++ compiler... yes >>> checking whether g++ accepts -g... yes >>> configure: Preparing to compile Graphviz. >>> configure: Configuring bundled Graphviz. >>> checking build system type... x86_64-unknown-linux-gnu >>> checking host system type... x86_64-unknown-linux-gnu >>> checking for a BSD-compatible install... /usr/bin/install -c >>> checking whether build environment is sane... yes >>> checking for a thread-safe mkdir -p... /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=gnu99 >>> 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=gnu99 accepts -g... yes >>> checking for gcc -std=gnu99 option to accept ISO C89... none needed >>> checking dependency style of gcc -std=gnu99... 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... /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... no >>> checking for tclsh8.5... /usr/bin/tclsh8.5 >>> checking whether gcc -std=gnu99 and cc understand -c and -o together... >>> yes >>> checking whether we are using the GNU C++ compiler... yes >>> checking whether g++ accepts -g... yes >>> checking dependency style of g++... gcc3 >>> checking for gcc... gcc >>> checking whether we are using the GNU Objective C compiler... no >>> checking whether gcc accepts -g... no >>> 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 -std=gnu99 -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... /bin/sed >>> checking for fgrep... grep -F >>> checking for ld used by gcc -std=gnu99... /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=gnu99 >>> object... ok >>> checking for dlfcn.h... yes >>> checking whether we are using the GNU C++ compiler... (cached) yes >>> checking whether g++ accepts -g... (cached) yes >>> checking dependency style of g++... (cached) gcc3 >>> checking how to run the C++ preprocessor... g++ -E >>> checking for objdir... .libs >>> checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no >>> checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC >>> checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes >>> checking if gcc -std=gnu99 static flag -static works... yes >>> checking if gcc -std=gnu99 supports -c -o file.o... yes >>> checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes >>> checking whether the gcc -std=gnu99 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... no >>> checking for dlopen in -ldl... yes >>> checking whether a program can dlopen itself... yes >>> checking whether a statically linked program can dlopen itself... no >>> checking whether stripping libraries is possible... yes >>> checking if libtool supports shared libraries... yes >>> checking whether to build shared libraries... no >>> checking whether to build static libraries... yes >>> checking for ld used by g++... /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++ linker (/usr/bin/ld -m elf_x86_64) supports >>> shared libraries... yes >>> checking for g++ option to produce PIC... -fPIC -DPIC >>> checking if g++ PIC flag -fPIC -DPIC works... yes >>> checking if g++ static flag -static works... yes >>> checking if g++ supports -c -o file.o... yes >>> checking if g++ supports -c -o file.o... (cached) yes >>> checking whether the g++ 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/i386-linux-gnu/mesa /lib/i386-linux-gnu >>> /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux- gnu >>> /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu >>> /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 >>> /usr/lib32 /libx32 /usr/libx32 /home/km/lib >>> checking for library containing dlopen... -ldl >>> checking for dlerror... yes >>> checking for shl_load... (cached) no >>> checking for shl_load in -ldld... (cached) no >>> checking for dld_link in -ldld... no >>> checking for _ prefix in compiled symbols... no >>> checking whether deplibs are loaded by dlopen... yes >>> checking for argz.h... yes >>> checking for error_t... yes >>> checking for argz_add... yes >>> checking for argz_append... yes >>> checking for argz_count... yes >>> checking for argz_create_sep... yes >>> checking for argz_insert... yes >>> checking for argz_next... yes >>> checking for argz_stringify... yes >>> checking if argz actually works... yes >>> checking whether libtool supports -dlopen/-dlpreopen... yes >>> checking for 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... no >>> checking for strlcpy... no >>> checking for X... disabled >>> configure: WARNING: X11 not available. >>> checking tcl.h usability... no >>> checking tcl.h presence... no >>> checking for tcl.h... no >>> configure: WARNING: Unable to find header tcl.h. The Tcl packages will >>> not be built >>> configure: WARNING: No Tcl. The Tk packages will not be built either >>> checking for connect... yes >>> checking for gethostbyname... yes >>> checking for main in -lXpm... yes >>> checking X11/Intrinsic.h usability... yes >>> checking X11/Intrinsic.h presence... yes >>> checking for X11/Intrinsic.h... yes >>> checking for X11/Xaw/Text.h... yes >>> checking for main in -lXaw... yes >>> checking zlib.h usability... yes >>> checking zlib.h presence... yes >>> checking for zlib.h... yes >>> checking for main in -lz... yes >>> checking for deflateBound... no >>> checking for GDK_PIXBUF... no >>> checking for GTK... no >>> 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... qmake >>> checking for QTCORE... 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... yes >>> 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 >>> (/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl) >>> configure: running /bin/bash ./configure --disable-option-checking >>> '-- prefix=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix' >>> 'CC=gcc -std=gnu99' 'CXX=g++' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2' >>> 'LDFLAGS=-L/usr/local/lib' >>> '-- libdir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib' >>> '--includedir=/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/lib unix/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' >>> 'R_LIBS=/home/km/lib/R/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... /bin/mkdir -p >>> checking for gawk... gawk >>> checking whether make sets $(MAKE)... yes >>> checking build system type... x86_64-unknown-linux-gnu >>> checking host system type... x86_64-unknown-linux-gnu >>> checking for style of include used by make... GNU >>> checking for gcc... gcc -std=gnu99 >>> 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=gnu99 accepts -g... yes >>> checking for gcc -std=gnu99 option to accept ISO C89... none needed >>> checking dependency style of gcc -std=gnu99... gcc3 >>> checking for a sed that does not truncate output... /bin/sed >>> checking for grep that handles long lines and -e... /bin/grep >>> checking for egrep... /bin/grep -E >>> checking for fgrep... /bin/grep -F >>> checking for ld used by gcc -std=gnu99... /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=gnu99 >>> object... ok >>> checking how to run the C preprocessor... gcc -std=gnu99 -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=gnu99 supports -fno-rtti -fno-exceptions... no >>> checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC >>> checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes >>> checking if gcc -std=gnu99 static flag -static works... yes >>> checking if gcc -std=gnu99 supports -c -o file.o... yes >>> checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes >>> checking whether the gcc -std=gnu99 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... no >>> checking for dlopen in -ldl... yes >>> checking whether a program can dlopen itself... yes >>> checking whether a statically linked program can dlopen itself... no >>> checking whether stripping libraries is possible... yes >>> checking if libtool supports shared libraries... yes >>> checking whether to build shared libraries... no >>> checking whether to build static libraries... yes >>> checking which extension is used for runtime loadable modules... .so >>> checking which variable specifies run-time module search path... >>> LD_LIBRARY_PATH >>> checking for the default library search path... /lib64 /usr/lib64 /lib >>> /usr/lib /usr/lib/i386-linux-gnu/mesa /lib/i386-linux-gnu >>> /usr/lib/i386-linux-gnu /lib/i686-linux-gnu /usr/lib/i686-linux- gnu >>> /usr/local/lib /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu >>> /usr/lib/x86_64-linux-gnu/mesa-egl /usr/lib/x86_64-linux-gnu/mesa /lib32 >>> /usr/lib32 /libx32 /usr/libx32 /home/km/lib >>> checking for library containing dlopen... -ldl >>> checking for dlerror... yes >>> checking for shl_load... (cached) no >>> checking for shl_load in -ldld... (cached) no >>> checking for dld_link in -ldld... no >>> checking for _ prefix in compiled symbols... no >>> checking whether deplibs are loaded by dlopen... yes >>> checking for argz.h... yes >>> checking for error_t... yes >>> checking for argz_add... yes >>> checking for argz_append... yes >>> checking for argz_count... yes >>> checking for argz_create_sep... yes >>> checking for argz_insert... yes >>> checking for argz_next... yes >>> checking for argz_stringify... yes >>> checking if argz actually works... yes >>> checking whether libtool supports -dlopen/-dlpreopen... yes >>> checking for unistd.h... (cached) yes >>> checking for dl.h... no >>> checking for sys/dl.h... no >>> checking for dld.h... no >>> checking for mach-o/dyld.h... no >>> checking for dirent.h... yes >>> checking for closedir... yes >>> checking for opendir... yes >>> checking for readdir... yes >>> checking for strlcat... no >>> checking for strlcpy... no >>> checking that generated files are newer than configure... done >>> configure: creating ./config.status >>> config.status: creating Makefile >>> config.status: creating config.h >>> config.status: executing depfiles commands >>> config.status: executing libtool commands >>> >>> ---------------------------------------------------------------- >>> >>> graphviz-2.28.0 will be compiled with the following: >>> >>> options: >>> cgraph: No (disabled by default - experimental) >>> digcola: Yes >>> expat: No (disabled) >>> fontconfig: No (disabled) >>> freetype: No (disabled) >>> glut: No (disabled) >>> gts: No (disabled) >>> ipsepcola: No (disabled by default - C++ portability issues) >>> ltdl: No (disabled) >>> ortho: Yes >>> png: No (disabled) >>> jpeg: No (disabled) >>> sfdp: Yes >>> shared: No (disabled) >>> static: Yes >>> qt: No (QtCore not available) >>> >>> 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 (QtCore not available) >>> >>> 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: No (gdk_pixbuf library not available) >>> ghostscript: No (disabled) >>> glitz: No (disabled by default - incomplete) >>> gtk: No (gtk library not available) >>> lasi: No (disabled) >>> ming: No (disabled by default - incomplete) >>> pangocairo: No (disabled) >>> quartz: No (disabled by default - Mac only) >>> rsvg: No (disabled) >>> visio: No (disabled by default - experimental) >>> xlib: No (disabled or unavailable) >>> >>> language extensions: >>> gv_sharp: No (swig not available) >>> gv_go: No (disabled by default - experimental) >>> gv_guile: No (swig not available) >>> gv_io: No (disabled by default - no swig support yet) >>> gv_java: No (swig not available) >>> gv_lua: No (swig not available) >>> gv_ocaml: No (swig not available) >>> gv_perl: No (swig not available) >>> gv_php: No (swig not available) >>> gv_python: No (swig not available) >>> gv_python23: No (disabled by default - for multiversion installs) >>> gv_python24: No (disabled by default - for multiversion installs) >>> gv_python25: No (disabled by default - for multiversion installs) >>> gv_python26: No (disabled by default - for multiversion installs) >>> gv_python27: No (disabled by default - for multiversion installs) >>> gv_R: No (swig not available) >>> gv_ruby: No (swig not available) >>> gv_tcl: No (tcl not available) >>> >>> tcldot: No (tcl not available) >>> tclpathplan: No (tcl not available) >>> gdtclft: No (tcl not available) >>> tkspline: No (tk not available) >>> grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h >>> make install-recursive >>> make[1]: Entering directory >>> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' >>> Making install in libltdl >>> make[2]: Entering directory >>> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >>> make install-am >>> make[3]: Entering directory >>> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >>> /bin/bash ./libtool --tag=CC --mode=compile gcc -std=gnu99 >>> -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='<config.h>' -DLTDL -I. -I. -Ilibltdl >>> -I./libltdl -I./libltdl -g -O2 -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 -std=gnu99 -DHAVE_CONFIG_H -I. >>> "-DLT_CONFIG_H=<config.h>" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl >>> -g -O2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c >>> -fPIC -DPIC -o dlopen.o >>> In file included from libltdl/lt__private.h:52:0, >>> from loaders/dlopen.c:32: >>> libltdl/lt__dirent.h:84:7: error: expected '=', ',', ';', 'asm' or >>> '__attribute__' before '-' token >>> make[3]: *** [dlopen.lo] Error 1 >>> make[3]: Leaving directory >>> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >>> make[2]: *** [install] Error 2 >>> make[2]: Leaving directory >>> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz/libltdl' >>> make[1]: *** [install-recursive] Error 1 >>> make[1]: Leaving directory >>> `/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/graphviz' >>> make: *** [install] Error 2 >>> cp: cannot stat >>> '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/*': No such >>> file or directory >>> cp: cannot stat >>> '/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/lib/grap hviz/*': >>> No such file or directory >>> checking for grep that handles long lines and -e... /bin/grep >>> checking for egrep... /bin/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 zlib.h usability... yes >>> checking zlib.h presence... yes >>> checking for zlib.h... yes >>> checking for deflateBound in -lz... yes >>> checking for stdbool.h that conforms to C99... yes >>> checking for _Bool... yes >>> checking for whether compiler has bool... yes >>> configure: Using the following compilation and linking flags for >>> Rgraphviz >>> configure: PKG_CFLAGS= >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/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 >>> 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 >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/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 >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c agopen.c -o agopen.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c agread.c -o agread.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c agwrite.c -o agwrite.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c bezier.c -o bezier.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c doLayout.c -o doLayout.o >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o >>> graphvizVersion.c: In function ‘Rgraphviz_capabilities’: >>> graphvizVersion.c:19:5: warning: implicit declaration of function >>> ‘gvPluginList’ [-Wimplicit-function-declaration] >>> graphvizVersion.c:19:8: warning: assignment makes pointer from integer >>> without a cast [enabled by default] >>> graphvizVersion.c:28:8: warning: assignment makes pointer from integer >>> without a cast [enabled by default] >>> graphvizVersion.c:37:8: warning: assignment makes pointer from integer >>> without a cast [enabled by default] >>> graphvizVersion.c:46:8: warning: assignment makes pointer from integer >>> without a cast [enabled by default] >>> graphvizVersion.c:55:8: warning: assignment makes pointer from integer >>> without a cast [enabled by default] >>> gcc -std=gnu99 -I/home/km/lib/R/include -DNDEBUG -I/usr/local/include >>> -I/tmp/Rtmpfrt4sH/R.INSTALL116486513/Rgraphviz/src/libunix/include /graphviz >>> -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 >>> -DHAVE_BOOL=1 -fpic -g -O2 -c init.c -o init.o >>> gcc -std=gnu99 -shared -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 >>> >>> gcc: error: libxdot.a: No such file or directory >>> gcc: error: libgvplugin_dot_layout.a: No such file or directory >>> gcc: error: libgvplugin_neato_layout.a: No such file or directory >>> gcc: error: libgvplugin_core.a: No such file or directory >>> gcc: error: libgvc.a: No such file or directory >>> gcc: error: libpathplan.a: No such file or directory >>> gcc: error: libgraph.a: No such file or directory >>> gcc: error: libcdt.a: No such file or directory >>> make: *** [Rgraphviz.so] Error 1 >>> ERROR: compilation failed for package ‘Rgraphviz’ >>> * removing ‘/home/km/lib/R/library/Rgraphviz’ >>> >>> >>> The downloaded source packages are in >>> ‘/tmp/RtmpPVdgYk/downloaded_packages’ >>> >>> Updating HTML index of packages in '.Library' >>> Making 'packages.html' ... done >>> Old packages: 'snowfall' >>> Update all/some/none? [a/s/n]: n >>> >>> Warning message: >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>> installation of package ‘Rgraphviz’ had non-zero exit status >>> > >>> >>> Regards, >>> Krishna >>> >>> >>> On Thu, Dec 19, 2013 at 8:52 PM, Kasper Daniel Hansen < >>> kasperdanielhansen@gmail.com> wrote: >>> >>>> We want the full output from the installation, despite its length. >>>> Also, which version of gcc are you using? >>>> >>>> Best, >>>> Kaspe >>>> >>>> >>>> On Thu, Dec 19, 2013 at 11:28 AM, km <srikrishnamohan@gmail.com> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I am unable to install Rgraphviz as a dependency for gage package. >>>>> I am using R (3.0.2) and bioconductor 2.13. >>>>> >>>>> > >>>>> biocLite('Rgraphviz') >>>>> >>>>> BioC_mirror: http://bioconductor.org >>>>> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version >>>>> 3.0.2. >>>>> Installing package(s) 'Rgraphviz' >>>>> trying URL ' >>>>> >>>>> http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz _2.6.0.tar.gz >>>>> ' >>>>> Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) >>>>> opened URL >>>>> ... >>>>> ... >>>>> gcc -std=gnu99 -shared -L/usr/local/lib64 -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 >>>>> gcc: error: libxdot.a: No such file or directory >>>>> gcc: error: libgvplugin_dot_layout.a: No such file or directory >>>>> gcc: error: libgvplugin_neato_layout.a: No such file or directory >>>>> gcc: error: libgvplugin_core.a: No such file or directory >>>>> gcc: error: libgvc.a: No such file or directory >>>>> gcc: error: libpathplan.a: No such file or directory >>>>> gcc: error: libgraph.a: No such file or directory >>>>> gcc: error: libcdt.a: No such file or directory >>>>> make: *** [Rgraphviz.so] Error 1 >>>>> ERROR: compilation failed for package ‘Rgraphviz’ >>>>> * removing ‘/home/km/lib64/R/library/Rgraphviz’ >>>>> >>>>> The downloaded source packages are in >>>>> ‘/tmp/RtmpOFdCuI/downloaded_packages’ >>>>> Updating HTML index of packages in '.Library' >>>>> Making 'packages.html' ... done >>>>> Warning message: >>>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>>>> installation of package ‘Rgraphviz’ had non-zero exit status >>>>> >>>>> >>>>> >>>>> > sessionInfo() >>>>> R version 3.0.2 (2013-09-25) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> >>>>> Regards, >>>>> Krishna >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>>> >>> >> > [[alternative HTML version deleted]]
ADD REPLYlink written 5.1 years ago by Kasper Daniel Hansen6.4k
Answer: Rgraphviz installation issue
0
gravatar for Luo Weijun
5.1 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Hi Krishna, Rgraphviz is not really a dependency of gage, but rather one for pathview since gage imports one function from pathview. R forces to install all secondary dependencies somehow, even though it is just for a single imported function and those are not really needed. Of course, I would still appreciate Kasper?s taking care of the Rgraphviz installation problem since that?s needed for other packages. To help users like you to install and use gage more smoothly, I just updated gage and removed that single import from pathview. Therefore, now you don?t have to install all the secondary dependencies like Rgraphviz. You shall see the new version (2.12.1) in the following page the next day or so. Let me know if you still don?t see the update by next Monday. http://bioconductor.org/packages/release/bioc/html/gage.html HTH, Weijun -------------------------------------------- On Thu, 12/19/13, km wrote: Hi all, I am unable to install Rgraphviz as a dependency for gage package. I am using R (3.0.2) and bioconductor 2.13. > biocLite('Rgraphviz') BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'Rgraphviz' trying URL ' http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2.6.0 .tar.gz ' Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb) opened URL ... ... gcc -std=gnu99 -shared -L/usr/local/lib64 -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 gcc: error: libxdot.a: No such file or directory gcc: error: libgvplugin_dot_layout.a: No such file or directory gcc: error: libgvplugin_neato_layout.a: No such file or directory gcc: error: libgvplugin_core.a: No such file or directory gcc: error: libgvc.a: No such file or directory gcc: error: libpathplan.a: No such file or directory gcc: error: libgraph.a: No such file or directory gcc: error: libcdt.a: No such file or directory make: *** [Rgraphviz.so] Error 1 ERROR: compilation failed for package ?Rgraphviz? * removing ?/home/km/lib64/R/library/Rgraphviz? The downloaded source packages are in ?/tmp/RtmpOFdCuI/downloaded_packages? Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?Rgraphviz? had non-zero exit status > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Regards, Krishna
ADD COMMENTlink written 5.1 years ago by Luo Weijun1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 331 users visited in the last hour