Non Zero exit status while updating igraph package version on Rstudio server on Linux cent OS 6 server

General
,
1

ERROR: compilation failed for package ‘igraph’

  • removing ‘/home/mykampaign/R/x86_64-redhat-linux-gnu-library/3.5/igraph’
  • restoring previous ‘/home/mykampaign/R/x86_64-redhat-linux-gnu-library/3.5/igraph’
    Warning in install.packages :
    installation of package ‘igraph’ had non-zero exit status
    Please help on this , even I am not able to install ‘CollapsibleTree’, ‘influenceR’, ‘rgexf’, ‘DiagrammeR’, ‘data.tree’,leaflet packages on Rstudio server but on local Rstudio desktop version every package is working fine
    Thanks in Advance,
    Manohar
2

Hi Manohar, welcome!
Could you share the whole error message? We are missing the important part.

3

Hi andresrcs, I am getting following error when I am updating igraph package in rstudio server which is installed on linux cent os 6 server,I need to update that package because I am not able to install collapasble tree pkg which requires latest version of igraph .

* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -m64 -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 -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran -m64 accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -m64 accepts -g... yes
checking how to run the C++ preprocessor... g++ -m64 -E
checking for rintf... yes
checking for finite... yes
checking for expm1... yes
checking for rint... yes
checking for log2... yes
checking for logbl... yes
checking for snprintf... yes
checking for log1p... yes
checking for round... yes
checking for fmin... yes
checking for stpcpy... yes
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
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 whether stpcpy is declared... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking net/if.h usability... yes
checking net/if.h presence... yes
checking for net/if.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking net/if_dl.h usability... no
checking net/if_dl.h presence... no
checking for net/if_dl.h... no
checking sys/sockio.h usability... no
checking sys/sockio.h presence... no
checking for sys/sockio.h... no
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking for struct sockaddr.sa_len... no
checking for xml2-config... /usr/bin/xml2-config
checking for xmlSAXUserParseFile in -lxml2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for __gmpz_add in -lgmp... no
checking for glp_read_mps in -lglpk... no
configure: creating ./config.status
config.status: creating src/Makevars.tmp
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
gfortran -m64   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules  -c AMD/Source/amd.f -o AMD/Source/amd.o
Warning: Nonconforming tab character in column 1 of line 422
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.4\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c AMD/Source/amd_1.c -o AMD/Source/amd_1.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.4\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c AMD/Source/amd_2.c -o AMD/Source/amd_2.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.4\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -O2 -g -pipe -Wall -Wp,-DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.4\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c bipartite.c -o bipartite.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.2.4\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC   -c blas.c -o blas.o
g++ -m64  -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -DUSING_R -DIGRAPH_THREAD_LOCAL=/**/ -DNDEBUG -Iprpack -I. -Iinclude -DPRPACK_IGRAPH_SUPPORT -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bliss.cc -o bliss.o
In file included from bliss.cc:20:
bliss/graph.hh:326: error: ISO C++ forbids initialization of member ‘refine_equal_to_first’
bliss/graph.hh:326: error: making ‘refine_equal_to_first’ static
bliss/graph.hh:326: error: ISO C++ forbids in-class initialization of non-const static member ‘refine_equal_to_first’
make: *** [bliss.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/home/mykampaign/R/x86_64-redhat-linux-gnu-library/3.5/igraph’
* restoring previous ‘/home/mykampaign/R/x86_64-redhat-linux-gnu-library/3.5/igraph’
Warning in install.packages :
  installation of package ‘igraph’ had non-zero exit status
4

This looks like an incompatibility issue with your compiler, do you have gfortran installed in your system? If not, try installing it from a system terminal and then try to install igraph again.

yum install gcc-gfortran
5

Hey Andreas thanks for your suggestion , gcc fortran it is already there on my server, I installed old packages its working fine.

6

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