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]]