I put in this code:
install.packages("glmnet")
And it delivers this error message:
* installing *source* package 'glmnet' ...
** package 'glmnet' successfully unpacked and MD5 sums checked
** using staged installation
** libs
*** arch - i386
"c:/rtools40/mingw32/bin/"g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -I'C:/Users/zac.t8/OneDrive/Documents/R/win-library/4.0/RcppEigen/include' -I'C:/Users/zac.t8/OneDrive/Documents/R/win-library/4.0/Rcpp/include' -Iglmnetpp/include -Iglmnetpp/src -Iglmnetpp/test -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
sh: c:/rtools40/mingw32/bin/g++: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.4/etc/i386/Makeconf:229: RcppExports.o] Error 127
ERROR: compilation failed for package 'glmnet'
* removing 'C:/Users/zac.t8/OneDrive/Documents/R/win-library/4.0/glmnet'
Warning in install.packages :
installation of package ‘glmnet’ had non-zero exit status
Can someone point out what is wrong? Thanks!
Related
> install.packages(c("lubridate", "nlme", "readxl", "sourcetools", "utf8", "xfun"))
Installing packages into ‘C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
There are binary versions available but the source versions are later:
binary source needs_compilation
lubridate 1.9.1 1.9.2 TRUE
nlme 3.1-161 3.1-162 TRUE
readxl 1.4.1 1.4.2 TRUE
sourcetools 0.1.7 0.1.7-1 TRUE
utf8 1.2.2 1.2.3 TRUE
xfun 0.36 0.37 TRUE
installing the source packages ‘lubridate’, ‘nlme’, ‘readxl’, ‘sourcetools’, ‘utf8’, ‘xfun’
trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.9.2.tar.gz'
Content type 'application/x-gzip' length 427200 bytes (417 KB)
downloaded 417 KB
trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-162.tar.gz'
Content type 'application/x-gzip' length 848546 bytes (828 KB)
downloaded 828 KB
trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.4.2.tar.gz'
Content type 'application/x-gzip' length 2091835 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/sourcetools_0.1.7-1.tar.gz'
Content type 'application/x-gzip' length 24095 bytes (23 KB)
downloaded 23 KB
trying URL 'https://cran.rstudio.com/src/contrib/utf8_1.2.3.tar.gz'
Content type 'application/x-gzip' length 241412 bytes (235 KB)
downloaded 235 KB
trying URL 'https://cran.rstudio.com/src/contrib/xfun_0.37.tar.gz'
Content type 'application/x-gzip' length 130063 bytes (127 KB)
downloaded 127 KB
* installing *source* package 'lubridate' ...
** package 'lubridate' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c datetime.c -o datetime.o
/bin/sh: line 1: gcc: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:253: datetime.o] Error 127
ERROR: compilation failed for package 'lubridate'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/lubridate'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/lubridate'
Warning in install.packages :
installation of package ‘lubridate’ had non-zero exit status
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -c chol.f -o chol.o
make: gfortran: No such file or directory
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:277: chol.o] Error 127
ERROR: compilation failed for package 'nlme'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/nlme'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/nlme'
Warning in install.packages :
installation of package ‘nlme’ had non-zero exit status
* installing *source* package 'readxl' ...
** package 'readxl' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -Iwindows -I. -D__USE_MINGW_ANSI_STDIO -I'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/cpp11/include' -I'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/progress/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp11.cpp -o cpp11.o
/bin/sh: line 1: g++: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:260: cpp11.o] Error 127
ERROR: compilation failed for package 'readxl'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/readxl'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/readxl'
Warning in install.packages :
installation of package ‘readxl’ had non-zero exit status
* installing *source* package 'sourcetools' ...
** package 'sourcetools' successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I../inst/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Reader.cpp -o Reader.o
/bin/sh: line 1: g++: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:260: Reader.o] Error 127
ERROR: compilation failed for package 'sourcetools'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/sourcetools'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/sourcetools'
Warning in install.packages :
installation of package ‘sourcetools’ had non-zero exit status
* installing *source* package 'utf8' ...
** package 'utf8' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -Iutf8lite/src -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c as_utf8.c -o as_utf8.o
/bin/sh: line 1: gcc: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:253: as_utf8.o] Error 127
ERROR: compilation failed for package 'utf8'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/utf8'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/utf8'
Warning in install.packages :
installation of package ‘utf8’ had non-zero exit status
* installing *source* package 'xfun' ...
** package 'xfun' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"C:/PROGRA~1/R/R-42~1.2/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
/bin/sh: line 1: gcc: command not found
make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:253: base64.o] Error 127
ERROR: compilation failed for package 'xfun'
* removing 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/xfun'
* restoring previous 'C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2/xfun'
Warning in install.packages :
installation of package ‘xfun’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\Sachin Dahiya\AppData\Local\Temp\RtmpgBGXsJ\downloaded_packages’
I am using R version 4.2.2 and R tools43 on Windows 11. These packages have been asking for updates for a while now but the compliation fails every time. Please let me know how to fix this issue. I have instaled R tools and R.4.2.2 in C:\Program Files\R.
These are my paths:
> .libPaths()
[1] "C:/Users/Sachin Dahiya/AppData/Local/R/win-library/4.2"
[2] "C:/Program Files/R/R-4.2.2/library"
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 trying to install some packages such Rcmdr or factoextra while on R in terminal (after upgrade to R 4.0.0 on Archlabs) the following errors shows up:
* installing *source* package ‘SparseM’ ...
** package ‘SparseM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -c bckslv.f -o bckslv.o
/usr/local/bin/gfortran: /usr/local/bin/gfortran: cannot execute binary file
make: *** [/usr/lib64/R/etc/Makeconf:190: bckslv.o] Error 126
ERROR: compilation failed for package ‘SparseM’
* removing ‘/usr/lib/R/library/SparseM’
and this one :
* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -I. -Ircon -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c Collector.cpp -o Collector.o
In file included from /usr/lib/R/library/Rcpp/include/Rcpp.h:77,
from Collector.cpp:1:
/usr/lib/R/library/Rcpp/include/Rcpp/Rmath.h: In function ‘double R::pythag(double, double)’:
/usr/lib/R/library/Rcpp/include/Rcpp/Rmath.h:222:57: error: ‘::Rf_pythag’ has not been declared; did you mean ‘pythag’?
222 | inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }
| ^~~~~~~~~
| pythag
make: *** [/usr/lib64/R/etc/Makeconf:176: Collector.o] Error 1
then followed by a bunch of
ERROR: dependencies ‘dendextend’, ‘FactoMineR’, ‘ggpubr’, ‘ggrepel’, ‘tidyr’ are not available for package ‘factoextra’
* removing ‘/usr/lib/R/library/factoextra’
following each dependencies produces the same errors with different new dependencies.
P.S: I'm a normie so please bear with me.
I had a similar error while installing 'ape'. For me it worked to reinstall the current version of the 'Rcpp' package:
install.packages('Rcpp')
Hope it works for you too !
I just installed R on linux. Now I try to install some packages on it. When I try on install the
the RCurl package using:
install.packages("RCurl")
I however get the following:
* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c bit-ops.c -o bit-ops.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c cksum.c -o cksum.o
gcc -std=gnu99 -shared -o bitops.so bit-ops.o cksum.o -L/usr/lib/R/lib -lR
installing to /home/marc/R/x86_64-pc-linux-gnu-library/3.0/bitops/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (bitops)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/marc/R/x86_64-pc-linux-gnu-library/3.0/RCurl’
The downloaded source packages are in
‘/tmp/RtmpAXtKXQ/downloaded_packages’
Warning message:
In install.packages("RCurl") :
installation of package ‘RCurl’ had non-zero exit status
In the beginning everything seems to go fine but then I trows a non-zero exit status error. Any thoughts
what goes wrong here?