I am trying to use the package semPlot with R version 3.2.3 on Linux Mint. Is the only solution to downgrade my R-version? I have installed package XML without errors. UPDATE BELOW
ran: install.packages("semPlot",dependencies=T) errors:
....
g++ -I/usr/share/R/include -DNDEBUG -I"/home/king/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c minqa.cpp -o minqa.o
/bin/bash: g++: command not found
make: *** [minqa.o] Error 127
ERROR: compilation failed for package ‘minqa’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/minqa’
Warning in install.packages :
installation of package ‘minqa’ had non-zero exit status
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether the C++ compiler works... no
configure: error: in `/tmp/Rtmpw7bRnY/R.INSTALL5fd12b68373/nloptr':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/king/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppEigen.cpp -o RcppEigen.o
/bin/bash: g++: command not found
make: *** [RcppEigen.o] Error 127
ERROR: compilation failed for package ‘RcppEigen’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/RcppEigen’
Warning in install.packages :
installation of package ‘RcppEigen’ had non-zero exit status
ERROR: dependencies ‘minqa’, ‘nloptr’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/lme4’
Warning in install.packages :
installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘arm’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/arm’
Warning in install.packages :
installation of package ‘arm’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘rockchalk’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/rockchalk’
Warning in install.packages :
installation of package ‘rockchalk’ had non-zero exit status
ERROR: dependency ‘arm’ is not available for package ‘mi’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/mi’
Warning in install.packages :
installation of package ‘mi’ had non-zero exit status
ERROR: dependency ‘mi’ is not available for package ‘sem’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/sem’
Warning in install.packages :
installation of package ‘sem’ had non-zero exit status
ERROR: dependency ‘sem’ is not available for package ‘qgraph’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/qgraph’
Warning in install.packages :
installation of package ‘qgraph’ had non-zero exit status
ERROR: dependencies ‘qgraph’, ‘sem’, ‘rockchalk’ are not available for package ‘semPlot’
* removing ‘/home/king/R/x86_64-pc-linux-gnu-library/3.2/semPlot’
Warning in install.packages :
installation of package ‘semPlot’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpW1PZ2x/downloaded_packages’
UPDATE
Based on the comments I discovered I had to install:
sudo apt-get install gcc
sudo apt-get install g++
sudo apt-get install build-essential
I am now getting:
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
Thanks again to the comments I discovered I had to install:
sudo apt-get install liblapack-dev
which finally fixed my issues and I was able to install the package
Related
I'm new in R and I've been having some issues installing Hmisc package in order to elaborate a Spearman's correlation heatmap. The warning and error are as follows:
18 warnings generated.
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c bilinear.f -o bilinear.o
make: gfortran: No such file or directory
make: *** [bilinear.o] Error 1
ERROR: compilation failed for package ‘interp’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/interp’
Warning in install.packages :
installation of package ‘interp’ had non-zero exit status
* installing *source* package ‘polspline’ ...
** package ‘polspline’ 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 allpack.f -o allpack.o
make: gfortran: No such file or directory
make: *** [allpack.o] Error 1
ERROR: compilation failed for package ‘polspline’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/polspline’
Warning in install.packages :
installation of package ‘polspline’ had non-zero exit status
* installing *source* package ‘VGAM’ ...
** package ‘VGAM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c VGAM_init.c -o VGAM_init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c caqo3.c -o caqo3.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ei.f -o ei.o
make: gfortran: No such file or directory
make: *** [ei.o] Error 1
ERROR: compilation failed for package ‘VGAM’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/VGAM’
Warning in install.packages :
installation of package ‘VGAM’ had non-zero exit status
ERROR: dependency ‘interp’ is not available for package ‘latticeExtra’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/latticeExtra’
Warning in install.packages :
installation of package ‘latticeExtra’ had non-zero exit status
ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Hmisc’
Warning in install.packages :
installation of package ‘Hmisc’ had non-zero exit status
ERROR: dependencies ‘Hmisc’, ‘polspline’ are not available for package ‘rms’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rms’
Warning in install.packages :
installation of package ‘rms’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/8b/43x_77fx1p73gb68h2418m5r0000gn/T/RtmpIhACeD/downloaded_packages.
PS. I'm also a Mac user, and I've trying to solve it as some of you guys have suggested in other similar questions,
I've used:
-adding dependencies=true in the script.
-installing tydiverse package
-installing backports
I haven't been able to install any packages (such as randomForest, devtools, etc.)
I have also updated my R to 4.2 recently (not sure if they are related). I am also running Ubuntu.
I suspect it was something to do with the C++ compiler, such as the g++ and GCC.
things that I have done:
I have edit the Makevars to include:
CC=/usr/bin/gcc
CXX=/usr/bin/g++
FC=/usr/bin/gfortran
F77=/usr/bin/gfortran
Is there anyone facing the same problem? or any hints and guidance are really appreciated. Thank you in advance. If you need more information, please kindly let me know.
One of the errors is (installing devtools):
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Reader.cpp -o Reader.o
g++: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: Reader.o] Error 1
ERROR: compilation failed for package ‘sourcetools’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/sourcetools’
Warning in install.packages :
installation of package ‘sourcetools’ had non-zero exit status
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
** using staged installation
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the fontconfig freetype2 library. Try installing:
* deb: libfontconfig1-dev (Debian, Ubuntu, etc)
* rpm: fontconfig-devel (Fedora, EPEL)
* csw: fontconfig_dev (Solaris)
* brew: freetype (OSX)
If fontconfig freetype2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:10: fatal error: fontconfig/fontconfig.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘systemfonts’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/systemfonts’
Warning in install.packages :
installation of package ‘systemfonts’ had non-zero exit status
* installing *source* package ‘gert’ ...
** package ‘gert’ successfully unpacked and MD5 sums checked
** using staged installation
> curl::curl_download("https://r-lib.github.io/gert/get-libgit2-linux.sh","get-libgit2-linux.sh")
>
>
Using static libgit2-1.1.0 for Linux x86_64
Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpNHz5pp/R.INSTALL48c6b475a68c2/gert/libgit2/include
Using PKG_LIBS=-L/tmp/RtmpNHz5pp/R.INSTALL48c6b475a68c2/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 -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpNHz5pp/R.INSTALL48c6b475a68c2/gert/libgit2/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c branch.c -o branch.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: branch.o] Error 1
ERROR: compilation failed for package ‘gert’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/gert’
Warning in install.packages :
installation of package ‘gert’ had non-zero exit status
* installing *source* package ‘commonmark’ ...
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/html.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o extensions.o init.o wrapper.o commonmark.so cmark/libstatcmark.a
gcc -I"/usr/share/R/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c extensions.c -o extensions.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: extensions.o] Error 1
ERROR: compilation failed for package ‘commonmark’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/commonmark’
Warning in install.packages :
installation of package ‘commonmark’ had non-zero exit status
* installing *source* package ‘profvis’ ...
** package ‘profvis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pause.c -o pause.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: pause.o] Error 1
ERROR: compilation failed for package ‘profvis’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/profvis’
Warning in install.packages :
installation of package ‘profvis’ had non-zero exit status
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c capture.c -o capture.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: capture.o] Error 1
ERROR: compilation failed for package ‘rlang’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/rlang’
* restoring previous ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag needed.
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o
g++: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: RcppExports.o] Error 1
ERROR: compilation failed for package ‘later’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/later’
Warning in install.packages :
installation of package ‘later’ had non-zero exit status
ERROR: dependency ‘systemfonts’ is not available for package ‘textshaping’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/textshaping’
Warning in install.packages :
installation of package ‘textshaping’ had non-zero exit status
* installing *source* package ‘cachem’ ...
** package ‘cachem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-asoVQd/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cache.c -o cache.o
gcc: fatal error: cannot execute ‘as’: execvp: No such file or directory
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: cache.o] Error 1
ERROR: compilation failed for package ‘cachem’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/cachem’
Warning in install.packages :
installation of package ‘cachem’ had non-zero exit status
ERROR: dependency ‘gert’ is not available for package ‘usethis’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/usethis’
Warning in install.packages :
installation of package ‘usethis’ had non-zero exit status
* installing *source* package ‘pkgload’ ...
** package ‘pkgload’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace ‘rlang’ 1.0.2 is being loaded, but >= 1.0.3 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘pkgload’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/pkgload’
* restoring previous ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependency ‘later’ is not available for package ‘promises’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/promises’
Warning in install.packages :
installation of package ‘promises’ had non-zero exit status
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/ragg’
Warning in install.packages :
installation of package ‘ragg’ had non-zero exit status
ERROR: dependency ‘cachem’ is not available for package ‘memoise’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/memoise’
Warning in install.packages :
installation of package ‘memoise’ had non-zero exit status
ERROR: dependency ‘commonmark’ is not available for package ‘roxygen2’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/roxygen2’
Warning in install.packages :
installation of package ‘roxygen2’ had non-zero exit status
ERROR: dependencies ‘promises’, ‘later’ are not available for package ‘httpuv’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/httpuv’
Warning in install.packages :
installation of package ‘httpuv’ had non-zero exit status
ERROR: dependency ‘memoise’ is not available for package ‘downlit’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/downlit’
Warning in install.packages :
installation of package ‘downlit’ had non-zero exit status
ERROR: dependencies ‘httpuv’, ‘sourcetools’, ‘later’, ‘promises’, ‘commonmark’, ‘cachem’ are not available for package ‘shiny’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/shiny’
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
ERROR: dependencies ‘downlit’, ‘memoise’, ‘ragg’ are not available for package ‘pkgdown’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/pkgdown’
Warning in install.packages :
installation of package ‘pkgdown’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/miniUI’
Warning in install.packages :
installation of package ‘miniUI’ had non-zero exit status
ERROR: dependencies ‘usethis’, ‘memoise’, ‘miniUI’, ‘pkgdown’, ‘profvis’, ‘roxygen2’ are not available for package ‘devtools’
* removing ‘/home/cindy/R/x86_64-pc-linux-gnu-library/4.2/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpITL0q0/downloaded_packages’
When I tried to install the package "plotly", it returned the following error message:
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c assign.c -o assign.o
clang: error: unsupported option '-fopenmp'
make: *** [assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/data.table’
Warning in install.packages :
installation of package ‘data.table’ had non-zero exit status
ERROR: dependency ‘data.table’ is not available for package ‘plotly’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/plotly’
Warning in install.packages :
installation of package ‘plotly’ had non-zero exit status
After some quick search this seems to be due to an incompatibility with MacOS High Sierra? I was able to install other packages like 'ggplot2' though. I'm very new to R and would really appreciate any help!
The non-zero exit status simply indicates that there was an error during the installation of the "package".
File link : https://cran.r-project.org/src/contrib/plotly_4.8.0.tar.gz
Try with the following command:
install.packages('FILE_PATH', repos=NULL, type = "source",dependencies = TRUE)
Doing so, all the dependencies for the package will also be downloaded. Downloading from source will recompile the package and installs.
I am trying to install R GPU package "gpuR" and I get the following error message:
/usr/bin/ld: cannot find -lOpenCL
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'gpuR.so' failed
make: *** [gpuR.so] Error 1
ERROR: compilation failed for package ‘gpuR’
* removing ‘/home/fibrou/R/x86_64-pc-linux-gnu-library/3.4/gpuR’
Warning in install.packages :
installation of package ‘gpuR’ had non-zero exit status
When I try to install OpenCL, I get the following error message:
install.packages("OpenCL")
Installing package into ‘/home/fibrou/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/OpenCL_0.1-3.tar.gz'
Content type 'application/x-gzip' length 15524 bytes (15 KB)
downloaded 15 KB
installing source package ‘OpenCL’ ...
** package ‘OpenCL’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ocl.c -o ocl.o
ocl.c:6:23: fatal error: CL/opencl.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'ocl.o' failed
make: *** [ocl.o] Error 1
ERROR: compilation failed for package ‘OpenCL’
removing ‘/home/fibrou/R/x86_64-pc-linux-gnu-library/3.4/OpenCL’
Warning in install.packages :
installation of package ‘OpenCL’ had non-zero exit status
I am running the latest LTS version of Ubuntu: 16.04, as well as the latest version of RStudio (Version 1.1.383 ) and R (R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree") I can find.
Why am I not able to install the GPU packages? What am I doing wrong?
I installed RStudio and R on Ubuntu 16.04 (Xenial) Linux:
user#machine:~/.Rlibs$ R --version
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
My problem is that I am not able to install package "devtools". I get a series of errors and all my attempts to install required dependencies failed so far. It seems that packages cannot be found even though they are installed.
I would be really grateful for any help!
The errors occur when trying to install the "devtools" package in RStudio or using the R console:
install.packages("devtools")
These are the errors I am getting (leaving out the download output):
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rawmatch.c -o rawmatch.o
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’
/usr/lib/R/etc/Makeconf:132: recipe for target 'rawmatch.o' failed
make: *** [rawmatch.o] Error 1
ERROR: compilation failed for package ‘mime’
* removing ‘/home/user/.Rlibs/mime’
Warning in install.packages :
installation of package ‘mime’ had non-zero exit status
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/user/.Rlibs/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/user/.Rlibs/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’
/usr/lib/R/etc/Makeconf:132: recipe for target 'aes.o' failed
make: *** [aes.o] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/home/user/.Rlibs/digest’
Warning in install.packages :
installation of package ‘digest’ had non-zero exit status
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’
/usr/lib/R/etc/Makeconf:132: recipe for target 'base64.o' failed
make: *** [base64.o] Error 1
ERROR: compilation failed for package ‘jsonlite’
* removing ‘/home/user/.Rlibs/jsonlite’
Warning in install.packages :
installation of package ‘jsonlite’ had non-zero exit status
* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for library containing inflate... no
configure: error: in `/tmp/RtmpMyvGHt/R.INSTALL4c4a1e9555fc/git2r':
configure: error:
---------------------------------------------
The zlib library that is required to build
git2r was not found.
Please install:
zlib1g-dev (package on e.g. Debian and Ubuntu)
zlib-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the zlib library is installed on your
system but the git2r configuration is
unable to find it, you can specify the
include and lib path to zlib with:
R CMD INSTALL --configure-args='--with-zlib-include=INCLUDE_PATH --with-zlib-lib=LIB_PATH' git2r
---------------------------------------------
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/home/user/.Rlibs/git2r’
Warning in install.packages :
installation of package ‘git2r’ had non-zero exit status
ERROR: dependencies ‘jsonlite’, ‘mime’, ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/user/.Rlibs/httr’
Warning in install.packages :
installation of package ‘httr’ had non-zero exit status
ERROR: dependency ‘digest’ is not available for package ‘memoise’
* removing ‘/home/user/.Rlibs/memoise’
Warning in install.packages :
installation of package ‘memoise’ had non-zero exit status
ERROR: dependencies ‘httr’, ‘memoise’, ‘digest’, ‘jsonlite’, ‘git2r’ are not available for package ‘devtools’
* removing ‘/home/user/.Rlibs/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
I noticed the following error:
gcc: error: unrecognized command line option ‘-fstack-protector-strong’
gcc: error: unrecognized command line option ‘-Wdate-time’
I experienced the same issue when I wanted to use an outdated version of gcc (specifically, 4.8) to resolve some compatibility issues in one of my projects. The compiler flags "-Wdate-time" and "-fstack-protector-strong" are not available in older gcc releases. A similar flag "-fstack-protector-all" is available in some older gcc releases though.
To wrap up, this error messages is due to the fact that the developers expected an up-to-date gcc and used compiler flags for that up-to-date gcc version, but the gcc installed in your system was outdated.
Hope that helps other who might run into this issue in the future.