I am getting error while installing topicmodels package in R.
on running install.packages("topicmodels",dependencies=TRUE) following are the last few lines I am getting. Please help. My R version is 3.1.3.
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c utilities.cpp -o utilities.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o topicmodels.so cokus.o common.o ctm.o dataset.o gsl-wrappers.o inference.o lda-alpha.o lda-inference.o lda-model.o model.o rGibbslda.o rctm.o rlda.o utilities.o utils.o -lgsl -lgslcblas -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/topicmodels/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/topicmodels/libs/topicmodels.so':
libgsl.so.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/topicmodels’
Warning message:
In install.packages("http://cran.r-project.org/src/contrib/topicmodels_0.2-1.tar.gz", :
installation of package ‘/tmp/RtmpbX6uuH/downloaded_packages/topicmodels_0.2-1.tar.gz’ had non-zero exit status
I have searched for this error at many places but haven't found solution. Please help
You don't have GSL installed:
sudo apt-get install gsl-bin libgsl0-dev
Related
I'm trying to install the pcadapt in RStudio using
> remotes::install_github("bcm-uga/pcadapt")
But it gives me the error installation of package ‘bigutilsr’ had non-zero exit status
Downloading GitHub repo bcm-uga/pcadapt#master
Installing 1 packages: bigutilsr
Installing package into ‘/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
probando la URL 'https://cloud.r-project.org/src/contrib/bigutilsr_0.3.2.tar.gz'
Content type 'application/x-gzip' length 915116 bytes (893 KB)
==================================================
downloaded 893 KB
* installing *source* package ‘bigutilsr’ ...
** package ‘bigutilsr’ successfully unpacked and MD5 sums checked
** libs
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogk.cpp -o ogk.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rollmean.cpp -o rollmean.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowSumsSq.cpp -o rowSumsSq.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o bigutilsr.so RcppExports.o ogk.o rollmean.o rowSumsSq.o -L/usr/lib/R/lib -lR
installing to /home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/bigutilsr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: S3 methods ‘eigs.matrix’, ‘eigs.dgeMatrix’, ‘eigs.dgCMatrix’, ‘eigs.dgRMatrix’, ‘eigs.dsyMatrix’, ‘eigs.dsCMatrix’, ‘eigs.dsRMatrix’, ‘eigs.function’, ‘eigs_sym.matrix’, ‘eigs_sym.dgeMatrix’, ‘eigs_sym.dgCMatrix’, ‘eigs_sym.dgRMatrix’, ‘eigs_sym.function’, ‘svds.matrix’, ‘svds.dgeMatrix’, ‘svds.dgCMatrix’, ‘svds.dgRMatrix’, ‘svds.dsyMatrix’, ‘svds.dsCMatrix’, ‘svds.dsRMatrix’, ‘svds.function’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) :
shared object ‘RSpectra.so’ not found
ERROR: lazy loading failed for package ‘bigutilsr’
* removing ‘/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/bigutilsr’
Error: Failed to install 'pcadapt' from GitHub:
(convertido del aviso) installation of package ‘bigutilsr’ had non-zero exit status
>
I've been searching on google and it seems that if gcc isn't set up correctly, then R tries to compile the packages and it fails (https://community.rstudio.com/t/cannot-install-any-packages-non-zero-exit-status/53310), but I don't know if this is the case, and if it is, I don't know how to solve it.
gcc --version
gcc (Debian 8.3.0-6) 8.3.0
I'm also having similar issues while trying to install adegenet, hierfstat, pegas, poppr and other packages but I will put a post about this with moor details somewhere else ins stackoverflow just to keep it simple and to not give place to confussion with the code.
If somebody can help me, I will appreciate it very much
Cheers
Upon executing 'Rscript -e "install.packages('mclust')"` with R 4.0.1 on Ubuntu 20.04, the process hangs during package preparation. Any idea how to fix or debug this issue?
ENV: R v4.0.1, GCC v9, Ubuntu v20.04
CMD: Rscript -e "install.packages('mclust')"
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/mclust_5.4.6.tar.gz'
Content type 'application/x-gzip' length 2877519 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -c dmvnorm.f -o dmvnorm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -c mclust.f -o mclust.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -c mclustaddson.f -o mclustaddson.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-mclust/00new/mclust/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Based on the response on R-sig-debian for a similar issue, I figured this issue is due to a bug in the pthread-based versions of Blas and Lapack libraries.
Until the bug is fixed, the workaround is to use libopenblas-openmp-blas and libopenblas-openmp-lapack libraries.
There are two ways to achieve use these libraries.
Uninstall the pthread-based version of the libraries and install the openmp-based version of the libraries.
Switch to openmp-based version of the libraries via update-alternatives. This can be done via sudo update-alternatives --config <name> command with being liblapack.so.3-x86_64-linux-gnu and libblas.so.3-x86_64-linux-gnu.
I am using this site for reference:
http://r4ds.had.co.nz/introduction.html
but I am unable to install the tidyverse package. Using dependencies = TRUE did not help. What else can I do?
installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
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/akriti/R/x86_64-pc-linux-gnu-library/3.2/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
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#1.1 (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/akriti/R/x86_64-pc-linux-gnu-library/3.2/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘evaluate’ ...
** package ‘evaluate’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (evaluate)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (highr)
* installing *source* package ‘markdown’ ...
** package ‘markdown’ 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 Rbase64.c -o Rbase64.o
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 Rinit.c -o Rinit.o
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 Rmarkdown.c -o Rmarkdown.o
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 autolink.c -o autolink.o
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 buffer.c -o buffer.o
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 houdini_href_e.c -o houdini_href_e.o
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 houdini_html_e.c -o houdini_html_e.o
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 html.c -o html.o
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 html_smartypants.c -o html_smartypants.o
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 markdown.c -o markdown.o
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 stack.c -o stack.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdini_html_e.o html.o html_smartypants.o markdown.o stack.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/markdown/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (markdown)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.c -o api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dumper.c -o dumper.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c emitter.c -o emitter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c implicit.c -o implicit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parser.c -o parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-ext.c -o r-ext.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scanner.c -o scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writer.c -o writer.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r-ext.o reader.o scanner.o writer.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c template.cpp -o template.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o htmltools.so RcppExports.o template.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/htmltools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (htmltools)
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ 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 base64.c -o base64.o
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 uriencode.c -o uriencode.o
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 utf8.c -o utf8.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o base64enc.so base64.o uriencode.o utf8.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/base64enc/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (base64enc)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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 ‘xml2’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GifTools.cpp -o GifTools.o
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 runfunc.c -o runfunc.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/caTools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (caTools)
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rprojroot)
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/httr’
Warning in install.packages :
installation of package ‘httr’ had non-zero exit status
* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (knitr)
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/rvest’
Warning in install.packages :
installation of package ‘rvest’ had non-zero exit status
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rmarkdown)
ERROR: dependencies ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/tidyverse’
Warning in install.packages :
*installation of package ‘tidyverse’ had non-zero exit status
You find the answer in your error message:
------------------------ ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
....
....
Copy and paste the following to your Terminal and than try installing tidyverse again. Should solve the problem.
# Required for many packages
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev
The problem occurred because tidyverse has system dependencies (i.e., libcurl4-openssl-dev, libssl-dev, libxml2-dev). I wrote a blog post that explains the solution in more details.
try this , it helped me out
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev
A strategy I have found successful is to install R and R-Studio through anaconda (https://www.anaconda.com/). Create a separate environment for R and use the anaconda navigator to install R-Studio.
(Two great things about this approach: i) dependencies are automatically taken care of in the background ii) your working environment is sandboxed against accidents ... unless you're looking for trouble :-) )
I had the same issue with RStudio on Ubuntu 20.04 but switched to using R and R - Studio through anaconda.Tidyverse can be loaded without issues.
library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✓ ggplot2 3.3.5 ✓ purrr 0.3.4
✓ tibble 3.1.2 ✓ dplyr 1.0.7
✓ tidyr 1.1.3 ✓ stringr 1.4.0
✓ readr 1.4.0 ✓ forcats 0.5.1
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
I am no longer able to compile an R package from source, and this has never been a problem before today. This is what happens:
R CMD build BAMMtools
* checking for file ‘BAMMtools/DESCRIPTION’ ... OK
* preparing ‘BAMMtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘BAMMtools_2.1.0.tar.gz’
R CMD INSTALL BAMMtools
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘BAMMtools’ ...
** libs
make: Nothing to be done for 'all'.
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so':
/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so: invalid ELF header
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/BAMMtools’
* restoring previous ‘/usr/local/lib/R/site-library/BAMMtools’
This does not seem to be a problem with this R package in particular, as I am able to install the package from within R, as:
> install.packages('BAMMtools_2.1.0.tar.gz', repos=NULL)
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘BAMMtools’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cohort_matrix.c -o cohort_matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dtrates.c -o dtrates.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c jenksBrks.c -o jenksBrks.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c treetraverse.c -o treetraverse.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BAMMtools.so cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BAMMtools)
I am running R v3.2.2, under Ubuntu v15.10 wily. I can't think of anything I've done within the last 24 hours that would have this effect, except updating my system with sudo apt-get update/upgrade.
Although this is not too much of a problem for installing the package, I can't run the R CMD check commands either, and this is a problem for development.
Any suggestions or advice would be greatly appreciated! Thanks!
As was found in the comments to the question, thanks to Jack Wasey, the problem was simply that I was running R CMD INSTALL on the name of the source directory, rather than on the built .tar.gz file.
While installing the package RcppArmadillo, I am getting below error.
installing to /usr/lib64/R/library/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'SHLIB.maker' not found
Error : unable to load R code in package ‘RcppArmadillo’
ERROR: lazy loading failed for package ‘RcppArmadillo’
* removing ‘/usr/lib64/R/library/RcppArmadillo’
Warning message:
In install.packages("RcppArmadillo_0.3.920.1.tar.gz", repos = NULL, :
installation of package ‘RcppArmadillo_0.3.920.1.tar.gz’ had non-zero exit status
You need to add R's repository to your system:
Use your favorite text editor (I'm using gedit as an example) to open /etc/apt/sources.list:
sudo gedit /etc/apt/sources.list
Add this line to the file (if this is slow, use another mirror. You may also want to change precise into the codename for your Ubuntu version --- e.g., trusty for 12.04):
deb http://cran.rstudio.com/bin/linux/ubuntu precise/
This works for me install.packages('RcppArmadillo')
> install.packages('RcppArmadillo')
Installing package into ‘/home/priyankara/R/i686-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://mirror.bjtu.edu.cn/cran/src/contrib/RcppArmadillo_0.5.300.4.tar.gz'
Content type 'application/octet-stream' length 967193 bytes (944 KB)
==================================================
downloaded 944 KB
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
* checking LAPACK_LIBS: divide-and-conquer complex SVD available via system LAPACK
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/priyankara/R/i686-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/priyankara/R/i686-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/priyankara/R/i686-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/priyankara/R/i686-pc-linux-gnu-library/3.2/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RcppArmadillo)