I am trying to install the digest package in R. However the installation is failing, apparently because the compiler does not recognize the -lgfortran flag. I have been unable to find any information on this. Any help is appreciated.
> install.packages('digest', repos='http://cran.us.r-project.org')
trying URL 'http://cran.us.r-project.org/src/contrib/digest_0.6.12.tar.gz'
Content type 'application/x-gzip' length 120337 bytes (117 KB)
==================================================
downloaded 117 KB
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c aes.c -o aes.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c crc32.c -o crc32.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c digest.c -o digest.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c init.c -o init.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c md5.c -o md5.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c raes.c -o raes.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c sha1.c -o sha1.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c sha2.c -o sha2.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c sha256.c -o sha256.o
gcc -std=gnu99 -I/home/alexander/anaconda3/lib/R/include -DNDEBUG -I/home/alexander/anaconda3/include -fpic -I/home/alexander/anaconda3/include -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/home/alexander/anaconda3/lib/R/lib -L/home/alexander/anaconda3/lib -lgfortran -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/home/alexander/anaconda3/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
/home/alexander/anaconda3/lib/R/share/make/shlib.mk:6: recipe for target 'digest.so' failed
make: *** [digest.so] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/home/alexander/anaconda3/lib/R/library/digest’
* restoring previous ‘/home/alexander/anaconda3/lib/R/library/digest’
use homebrew to install gcc, gfortrain
Create folder /Users/YOURNAME/.R
Create text file /Users/YOURNAME/.R/Makevars
Put this into that file:
FC = usr/local/opt/gcc/bin/gfortran
F77 = /usr/local/opt/gcc/bin/gfortran
FLIBS = -L/usr/local/opt/gcc/lib
Related
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
I want to install devtools in the Rstudio server, but failed all the time. Here are the results running the install.packages.
> install.packages("devtools")
Installing package into ‘/GPUFS/smu_ymyu_1/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘gert’, ‘usethis’
trying URL 'https://cran.rstudio.com/src/contrib/gert_1.9.1.tar.gz'
Content type 'application/x-gzip' length 121017 bytes (118 KB)
==================================================
downloaded 118 KB
trying URL 'https://cran.rstudio.com/src/contrib/usethis_2.1.6.tar.gz'
Content type 'application/x-gzip' length 342349 bytes (334 KB)
==================================================
downloaded 334 KB
trying URL 'https://cran.rstudio.com/src/contrib/devtools_2.4.5.tar.gz'
Content type 'application/x-gzip' length 374718 bytes (365 KB)
==================================================
downloaded 365 KB
* installing *source* package ‘gert’ ...
** package ‘gert’ successfully unpacked and MD5 sums checked
** using staged installation
Using static libgit2 for Linux x86_64
Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include
Using PKG_LIBS=-L/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/lib -lgit2 -lrt -lpthread -lssh2 -lssl -lcrypto -ldl -lpcre -lz
Configuration OK!
** libs
rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c branch.c -o branch.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c clone.c -o clone.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c commit.c -o commit.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c config.c -o config.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c conflicts.c -o conflicts.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c files.c -o files.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c merge.c -o merge.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rebase.c -o rebase.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c stash.c -o stash.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c submodules.c -o submodules.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c tag.c -o tag.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I"/app/centos/R/4.1.1/lib64/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o
gcc -std=gnu99 -shared -L/app/centos/R/4.1.1/lib64/R/lib -L/usr/local/lib64 -o gert.so branch.o clone.o commit.o config.o conflicts.o files.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o -L/tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/lib -lgit2 -lrt -lpthread -lssh2 -lssl -lcrypto -ldl -lpcre -lz -L/app/centos/R/4.1.1/lib64/R/lib -lR
/usr/bin/ld: /tmp/RtmpK20lPh/R.INSTALL10915eb5334/gert/libgit2/lib/libgit2.a(annotated_commit.c.o): unrecognized relocation (0x2a) in section `.text'
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
make: *** [gert.so] Error 1
ERROR: compilation failed for package ‘gert’
* removing ‘/GPUFS/smu_ymyu_1/R/x86_64-pc-linux-gnu-library/4.1/gert’
Warning in install.packages :
installation of package ‘gert’ had non-zero exit status
ERROR: dependency ‘gert’ is not available for package ‘usethis’
* removing ‘/GPUFS/smu_ymyu_1/R/x86_64-pc-linux-gnu-library/4.1/usethis’
Warning in install.packages :
installation of package ‘usethis’ had non-zero exit status
ERROR: dependency ‘usethis’ is not available for package ‘devtools’
* removing ‘/GPUFS/smu_ymyu_1/R/x86_64-pc-linux-gnu-library/4.1/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp7IpcmZ/downloaded_packages’
And I searched in the Internet, followed the previous suggestion to install the libgit2 in the Linux.
Linux version 3.10.0-957.el7.x86_64 (root#huawei-2u) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) ) #1 SMP Sat Oct 12 02:01:43 CST 2019
> $yum install libgit2
> $yum info libgit2
Loaded plugins: fastestmirror, ovl
ovl: Error while doing RPMdb copy-up:
[Errno 13] Permission denied: '/var/lib/rpm/.dbenv.lock'
Loading mirror speeds from cached hostfile
* epel: epel.mirror.angkasa.id
Available Packages
Name : libgit2
Arch : x86_64
Version : 0.26.8
Release : 1.el7_9
Size : 430 k
Repo : extras/7/x86_64
Summary : C implementation of the Git core methods as a library with a solid API
URL : http://libgit2.github.com/
License : GPLv2 with exceptions
Description : libgit2 is a portable, pure C implementation of the Git core methods
: provided as a re-entrant linkable library with a solid API, allowing
: you to write native speed custom Git applications in any language
: with bindings.
After installing the libgit2, but I still can't install the devtools in Rstudio server. Please help me.
I need to install nlme as it is a dependency for the MSstats package I need. I currently run on R version 4.2.0. When I try to install with Bioc manager I get the following:
> BiocManager::install("MSstats")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Old packages: 'nlme'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
nlme 3.1-157 3.1-158 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘nlme’
trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-158.tar.gz'
Content type 'application/x-gzip' length 845427 bytes (825 KB)
==================================================
downloaded 825 KB
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c chol.f -o chol.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c corStruct.c -o corStruct.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gnls.c -o gnls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c matrix.c -o matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nlOptimizer.c -o nlOptimizer.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nlme.c -o nlme.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nlmefit.c -o nlmefit.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pdMat.c -o pdMat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pythag.c -o pythag.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c rs.f -o rs.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [nlme.so] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/nlme’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/nlme’
The downloaded source packages are in
‘/private/var/folders/qx/5klvf6g112zb1vzzp5bt8n9r0000gn/T/Rtmpz9mEK5/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'MSstats'
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘nlme’ had non-zero exit status
I was installing another package called vcfR where it says vegan is source package and needs to be installed, then it showed errors when installing. So I decided to install vegan package first.
This is an online R studio, the package I need to analyse is too big to be done on my laptop. The online R studio is by my school server, which was in-built in a ssh server account.
below is the error message:
Installing package into ‘/home/joyzheng/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/vegan_2.5-7.tar.gz'
Content type 'application/x-gzip' length 2074611 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
* installing *source* package ‘vegan’ ...
** package ‘vegan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c data2hill.c -o data2hill.o
gfortran -fpic -g -O2 -c decorana.f -o decorana.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c getF.c -o getF.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c goffactor.c -o goffactor.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gfortran -fpic -g -O2 -c monoMDS.f -o monoMDS.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nestedness.c -o nestedness.o
gfortran -fpic -g -O2 -c ordering.f -o ordering.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pnpoly.c -o pnpoly.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c stepacross.c -o stepacross.o
gcc -std=gnu99 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vegdist.c -o vegdist.o
gcc -std=gnu99 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o vegan.so data2hill.o decorana.o getF.o goffactor.o init.o monoMDS.o nestedness.o ordering.o pnpoly.o stepacross.o vegdist.o -L/opt/R/4.0.3/lib/R/lib -lRlapack -L/opt/R/4.0.3/lib/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/opt/R/4.0.3/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [vegan.so] Error 1
ERROR: compilation failed for package ‘vegan’
* removing ‘/home/joyzheng/R/x86_64-pc-linux-gnu-library/4.0/vegan’
Warning in install.packages :
installation of package ‘vegan’ had non-zero exit status```
I tried to install the 'data.table' package with R 3.3.0, but it returns the given error as below. I installed all required packages, but it did not help me at all.
I googled for the same issue, but there's nothing.
Please share your experience to fix it, if you had the same problem. It is very strange to me now.
Thanks a lot,
Sean
> install.packages('data.table')
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3233k 100 3233k 0 0 2098k 0 0:00:01 0:00:01 --:--:-- 2205k
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c assign.c -o assign.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c between.c -o between.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c bmerge.c -o bmerge.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c chmatch.c -o chmatch.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c dogroups.c -o dogroups.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c fastmean.c -o fastmean.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c fcast.c -o fcast.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c fmelt.c -o fmelt.o
gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include -fopenmp -fpic -g -O2 -c forder.c -o forder.o
forder.c: In function ‘range_str’:
forder.c:296: error: expected end of line before ‘update’
make: *** [forder.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/usr/lib64/R/library/data.table’
The downloaded source packages are in
‘/tmp/RtmpCfSYUU/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("data.table") :
installation of package ‘data.table’ had non-zero exit status
It seems without Rstem and sentiment packages twitter sentiment analysis
is difficult.
I am trying this Rstem and sentiment packages installation using the tar.gz file
(as no windows binary available in omegahat or in the github of Timothy P. Jurka)
but it gives an error:
installation of package 'Rstem' had non-zero exit status
I tried even command prompt. That gives below error. Any clue how to solve it ? my system is windows 7, R 2.15, Rstudio.
D:\R Projects>R CMD INSTALL Rstem_0.4-1.tar.gz
* installing to library 'D:/R-Econometrics/R-2.15.1/library'
* installing *source* package 'Rstem' ...
** libs
*** arch - i386
D:/R-Econometrics/R-2.15.1/etc/i386/Makeconf:194: warning: overriding recipe for
target `.m.o'
D:/R-Econometrics/R-2.15.1/etc/i386/Makeconf:187: warning: ignoring old recipe f
or target `.m.o'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c api.c -o api.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c danish_stem.c -o danish_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c dutch_stem.c -o dutch_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c english_stem.c -o english_stem.o
english_stem.c: In function 'r_prelude':
english_stem.c:376:5: warning: label 'lab1' defined but not used
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c finnish_stem.c -o finnish_stem.o
finnish_stem.c: In function 'r_case':
finnish_stem.c:448:21: warning: unused variable 'm'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c french_stem.c -o french_stem.o
french_stem.c: In function 'french_stem':
french_stem.c:951:25: warning: unused variable 'm'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c german_stem.c -o german_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c mytest.c -o mytest.o
mytest.c: In function 'S_stemWords':
mytest.c:76:3: warning: pointer targets in passing argument 1 of 'Rf_mkChar' dif
fer in signedness
D:/R-Econometrics/R-2.15.1/include/Rinternals.h:628:6: note: expected 'const cha
r *' but argument is of type 'symbol *'
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c norwegian_stem.c -o norwegian_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c portuguese_stem.c -o portuguese_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c russian_stem.c -o russian_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c spanish_stem.c -o spanish_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c swedish_stem.c -o swedish_stem.o
gcc -I"D:/R-Econometrics/R-2.15.1/include" -DNDEBUG -I. -I../Snowball/q
-O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
process_begin: CreateProcess(NULL, basename Rstem.dll .dll, ...) failed.
process_begin: CreateProcess(NULL, basename Rstem.dll .dll, ...) failed.
process_begin: CreateProcess(NULL, basename Rstem.dll .dll, ...) failed.
"zapi.o danish_stem.o dutch_stem.o english_stem.o finnish_stem.o french_stem.o g
erman_stem.o mytest.o norwegian_stem.o portuguese_stem.o russian_stem.o spanish_
stem.o swedish_stem.o utilities.o" was unexpected at this time.
make: *** [Rstem.dll] Error 255
ERROR: compilation failed for package 'Rstem'
* removing 'D:/R-Econometrics/R-2.15.1/library/Rstem'