I try to install R packages by using devtools (for specific version) but got some errors.
I have to install packages that's specific version and use specific R version (4.1.*) plz.
R, devtools version
R version : 4.1.3
devtools: 2.4.4
Install packages
forecast : 8.13
kernlab : 0.9-29
Install commands
install_version("forecast", version = "8.13")
install_version("kernlab", version = "0.9-29")
or add option dependencies=TRUE
Error list
cc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I
'/usr/local/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2 -fdebug-prefix-ma
p=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-s
ecurity -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registerDynamicSymbol.c -o registerDynami
cSymbol.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcp
p/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2 -fde
bug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -We
rror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c updateMatrices.cpp -o update
Matrices.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcp
p/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -fpic -g -O2 -fde
bug-prefix-map=/build/r-base-NlA7dw/r-base-4.1.3=. -fstack-protector-strong -Wformat -We
rror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c updateTBATSMatrices.cpp -o u
pdateTBATSMatrices.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o forec
ast.so calcBATS.o calcTBATS.o etsTargetFunction.o etsTargetFunctionWrapper.o etscalc.o e
tspolyroot.o makeBATSMatrices.o makeTBATSMatrices.o registerDynamicSymbol.o updateMatric
es.o updateTBATSMatrices.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -l
R
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:10: recipe for target 'forecast.so' failed
make: *** [forecast.so] Error 1
ERROR: compilation failed for package ‘forecast’
* removing ‘/usr/local/lib/R/site-library/forecast’
경고메시지(들):
i.p(...)에서:
installation of package ‘/tmp/RtmpGgApec/remotes25555374bfb7/forecast’ had non-zero ex
it status
Commands I've tried
sudo apt-get install g++
sudo apt install gfortran
sudo apt install libcurl4-gnutls-dev
R version upgrade 4.1.0 -> 4.1.3
R version downgrade 4.1.3 -> 4.1.0
install.packages('forecast')
install.packages('kernlab')
Short answer: We supply a package with the most common dependencies so consider doing sudo apt-get install r-base-dev. After that you can compile.
Longer answer: Ubuntu contains a number of pre-built CRAN packages. Consider doing sudo apt install r-cran-kernlab r-cran-forecast. For an older Ubuntu release this may reflect older versions.
Best answer (if you are on Ubuntu 20.04 or 22.04): Consider r2u which has all (!!) of the CRAN packages as r-cran-binaries, and uses bspm so that you can just say install.packages(c("kernlab", "forecast")) and still get everything pre-made as binaries, with dependencies, and managed via apt. But we do not support 18.04 for that.
In general when libraries are missing, "cannot find -lXXX", you should apt-cache search libXXX + -dev, and apt-get install what you find.
So in this case:
sudo apt-get install libblas-dev
sudo apt-get install liblapack-dev
A related answer.
I've recently installed R version 4.0.5 (2021-03-31) onto Ubuntu 20.04.2 LTS. R is working as expected.
However, while some packages have installed without issue (e.g., R.matlab), there are several packages that have not been able to install. As as example, running install.packages("data.table") throws the following error:
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
gcc -std=gnu99 9.3.0
zlib 1.2.11 is available ok
R CMD SHLIB supports OpenMP without any extra hint
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c assign.c -o assign.o
during GIMPLE pass: ccp
assign.c: In function ‘memrecycle’:
assign.c:1205:1: internal compiler error: Segmentation fault
1205 | }
| ^
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-9/README.Bugs> for instructions.
make: *** [/usr/lib/R/etc/Makeconf:172: assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
I get similar errors (i.e., "internal compiler error") with other package installation attempts, but with slightly different output. For example, install.packages("xfun") throws the following error, truncated for brevity:
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-tRgc13/r-base-4.0.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
during GIMPLE pass: ccp
base64.c: In function ‘base64_decode_impl’:
base64.c:237:1: internal compiler error: Segmentation fault
237 | }
| ^
I have tried reinstalling gcc-9, which has not helped. I had found that the PATH in Sys.getenv("PATH") was pointing to a miniconda3 install on my system, so updated that to /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/rstudio/bin/postback, which also has not helped.
My goal is to install packages among those above without throwing these compiler errors. Any help would be greatly appreciated.
In case others also run into this issue in the future, I am posting the solution that was suggested to me by https://answers.launchpad.net/ubuntu. Here is the link to the question I posted: https://answers.launchpad.net/ubuntu/+question/696623.
The issue turned out to be that R was using gcc-9 rather than gcc-10 to compile packages. The older version of gcc was throwing an error. Here are the steps I took to solve the problem:
Install gcc-10, which was not available on my system: sudo apt install gcc-10.
Edit the CC= pointer in the /usr/lib/R/etc/Makeconf file to gcc-10: open Terminal, type sudo nano /usr/lib/R/etc/Makeconf and replace the current CC= to CC=gcc-10. Save the file.
Restart R and run the install.packages() command for those packages that were not compiling correctly.
EDIT: Please see the comments below for a discussion. The above steps resolve the issue, but are not recommended. The issue was related to R not using the system package manager to install packages when the call install.packages() was used in R.
Installing the package bspm solved the issue for me. This package and its utility is discussed here for those who are curious.
To use install.packages() within R, bspm can be used in two ways:
bspm::enable() within R and then install.packages()
As written in its documentation: To enable bspm system-wide by default, include the following: suppressMessages(bspm::enable()) into the Rprofile.site file.
Thanks very much to Dirk for his guidance.
I cannot install qpcR package, using this command in R:
install.packages("qpcR")
Apparently, everything looks fine initially:
Installing package into ‘/home/emanuel/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/qpcR_1.4-1.tar.gz'
Content type 'application/x-gzip' length 4303726 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
* installing *source* package ‘qpcR’ ...
** package ‘qpcR’ 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 registerDynamicSymbol.c -o registerDynamicSymbol.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 smth.c -o smth.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o qpcR.so registerDynamicSymbol.o smth.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
And then things starts to going wrong:
usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'qpcR.so' failed
make: *** [qpcR.so] Error 1
ERROR: compilation failed for package ‘qpcR’
* removing ‘/home/emanuel/R/x86_64-pc-linux-gnu-library/3.4/qpcR’
Warning in install.packages :
installation of package ‘qpcR’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpOPiQkB/downloaded_packages’
Additional (maybe) relevant info:
Before the lines presented above, I was having trouble with another qpcR dependence, the rgl package, and I solved trying all the suggestions from another question: "Error in installing rgl package".
I made a brief search about: "-llpack", "-lblas", "qpcR.so" .Unfortunately nothing seems (to me at least) to be related to my specific problem.
I using Mint with these specifications: Linux version 4.8.0-53-generic (buildd#lgw01-56) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) ) #56~16.04.1-Ubuntu
R version 3.4.4
R studio Version 1.1.453
Thanks in advance for any help!
satisfy the dependencies using this command in terminal.
sudo apt-get install libblas-dev liblapack-dev
hope this helps (Y)
I am trying to install an R package from source, but getting an error:
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c mclust.f -o mclust.o
gfortran-4.8 -fPIC -g -O2 -c mclustaddson.f -o mclustaddson.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 mclust.so mclust.o mclustaddson.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mclust.so] Error 1
ERROR: compilation failed for package ‘mclust’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mclust’
Warning in install.packages :
installation of package ‘mclust’ had non-zero exit status
I don't have /usr/local/lib/gcc/x86_64-apple-darwin13.0.0, so it makes sense that it can't be found. I have /usr/local/lib/gcc/i686-apple-darwin11 and /usr/local/lib/gcc/4.8 (symlink to Homebrew installation). Where is it getting x86_64-apple-darwin13.0.0 from?
There are a lot of references to a similar error online. However, all of them are related to compiling in Xcode and resolved by updating project settings, which is not applicable here.
You need to modify the ~/.R/Makevars file. For a greater overview of this see: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages
Alternatively, this has been answered before in a bit more depth by #kevin-ushey in Rcpp warning: "directory not found for option '-L/usr/local/Cellar/gfortran/4.8.2/gfortran'".
What is happening is your code is not being run under gcc instead it is being forwarded to clang
You will need to change your compile statements in ~/.R/Makevars/ to gcc using:
VER=-5.3.0
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/5.3.0/lib/gcc/5
This assumes you have already installed gcc via homebrew under:
brew install gcc
(gfortran ships with gcc in brew now)
Incorporating previous solutions with additional help from the comments, the following solution has worked for me on Mac OS X High Sierra.
Create/edit ~/.R/Makevars with the following contents:
VER=-8
CC=gcc$(VER)
CXX=g++$(VER)
CXX11=g++$(VER)
CXX14=g++$(VER)
CXX17=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8
Note, I am using homebrew and have gcc version 8.2.0 installed.
From http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/ you can fix this by downloading the optional gfortran libraries from http://r.research.att.com/libs/ and extracting them. To do this on the command line
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
I had this issue for a long time, working on a Mac. Following the other answers on this page and other questions, I did the following and it finally worked!
Step 1 - brew install gcc (it installed gcc-11 for me. If this is different for you in the future, replace gcc-11 below with the corresponding version. You can find the version by checking in the folder /usr/local/bin and seeing the latest gcc version file there)
Step 2 - xcode-select --install (this installs Xcode CLI)
Step 3 - ln -sf /usr/local/bin/gcc-11 /usr/local/bin/gcc (this makes a new gcc symlink under /usr/local/bin/. Source)
Step 4 - I did not have a ~/.R/Makevars file. Heck, I didn't even have the ~./R folder. Made the folder and the file. Here is what I wrote in the Makevars file (remember to change the GCC version in the first and last line according to the version you have. Also remember to not have the entire version number that's in the last line, in the first line. Just the overall version number - 11 in my case) -
VER=-11
CC=gcc$(VER)
CXX=g++$(VER)
CXX11=g++$(VER)
CXX14=g++$(VER)
CXX17=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/11.2.0_3/lib/gcc/11
Now restart, and voila! It works.
I'm working on MacOS Mojave (10.14.5) and on R 4.0.0. The problem here is that "CRAN R 4.0.0 builds and higher no longer use any custom compilers" (see here), so the Makevars solution does not appear to work anymore.
The solution for me was to download and install the GNU Fortran compiler from the official R-Project website. Note that you will also need Xcode and Xcode command-line tools.
After running the installer with default settings, compilation of gfortran code worked without problems.
I received the same error on MAC. All I needed to do was to install gfortran-6.1.pkg from https://cran.r-project.org/bin/macosx/tools/. Make sure that the package is installed under /usr/local/gfortran so it can be found by R.
Alternatively you can install it via homebrew typing brew cask install gfortran in the terminal (it may ask for your password).
In my case I combined this answer with this one, to produce the following code in the ~./R/.Makevars-file.
touch ~./R/.Makevars
(because it didn't exist there)
open -a BBEdit ~./R/.Makevars
(I use BBEdit as text editor)
Added the following lines to the Makevars-file:
VER=-11
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
# FLIBS=-L/usr/local/Cellar/gcc/11.1.0_1/lib/gcc/11
# FLIBS = -L`gfortran -print-file-name=libgfortran.dylib | xargs dirname`
FLIBS=`gfortran -print-search-dirs | grep ^libraries: | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`
These two lines were suggested by #KevinUshy.
# FLIBS=-L/usr/local/Cellar/gcc/11.1.0_1/lib/gcc/11
# FLIBS = -L`gfortran -print-file-name=libgfortran.dylib | xargs dirname`
I commented these out, as I figure that the final line would probably work best.
Two notes.
I have brew installed and I used brew to install gcc using the command brew install gcc.
I figure out the version-naming using brew info gcc, which gave me 11.1.0_1, but it is linked as gcc-11, so VER=-11 in the .Makevars-file.
Hope this helps others.
I am having Mac OS Catalina and in my case installation of Homebrew, the newest gcc and Gfortran 8.2.0 solved the issue.
The solution was to re-install problematic packages with Homebrew.
$ brew uninstall --ignore-dependencies --force openssl
$ brew install openssl
$ brew uninstall --ignore-dependencies --force readline
$ brew install readline
Digging this topic, if you tried these and much others approaches related to this error and got no success, I strongly recommend you to check if your OSx - just in case - deleted the .zshrc file.
If that's the case, you should create again this file in the root dir. type in your terminal:
touch .zshrc
followed by
openssl_prefix=$(brew --prefix openssl) printf "CFLAGS=-I$openssl_prefix/include \nLDFLAGS=-L$openssl_prefix/lib"
example of output:
CFLAGS=-I/usr/local/opt/openssl#3/include LDFLAGS=-L/usr/local/opt/openssl#3/lib
add them to the zshrcfile content, run
source .zshrc
to refresh the file and that`s all!
Had this problem using R on macos 12.4. It was caused by old and stale entries in my ~/.R/Makevars file. Once I commented everything out everything compiled just fine. I have XCode and brew install gcc active.
For later versions of R (R 4.0 and higher) and later operating systems, the recommended fix for this problem seems to be to install gfortran via rtools (see here, already mentioned in the answer of #lks_swrx).
When following these instructions, I ran into an additional problem, since my computer uses Apple Silicon chips (not Intel anymore), for which I wanted to add a solution here:
Download the appropriate gfortran tarball from rtools
Run tar fxz gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
Add it to your path by adding this line to your .zshrc file:
nano .zshrc (or whatever you use as text editor)
export PATH=$PATH:/opt/R/arm64/gfortran/bin
So far, so good; but the installation of DESeq2, which brought me here, did still not work, because R could not find the library. This is the fix:
Create a symlink to the gfortran library in /usr/local, so that R can find it:
ln -s /opt/R/arm64/gfortran /usr/local/gfortran (might require sudo)
I am using R in Ubuntu 10.04.
I need to understand the documentation.
Installing knncat I get this error message:
gcc -I/usr/share/R/include -I . -DUSE_R_ALLOC -DCALL_FROM_R -fpic
-std=gnu99 -O3 -pipe -g -c ranlib.c -o ranlib.o gcc -I/usr/share/R/include -I . -DUSE_R_ALLOC -DCALL_FROM_R -fpic -std=gnu99 -O3 -pipe -g -c utilsR.c -o utilsR.o gcc -shared -o knncat.so com.o dodisc.o donn.o donnwrap.o dsort.o linpack.o matrix.o
objective.o ords.o ranlib.o utilsR.o -llapack -lblas -lgfortran -lm
-L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -llapack collect2: ld returned 1 exit status make: *** [knncat.so] Error 1 ERROR:
compilation failed for package ‘knncat’
In the documentation I find this recomendation:
Provision is made for using an external LAPACK library, principally to
cope with BLAS libraries which contain a copy of LAPACK (such as sunperf
on Solaris, vecLib on OS X and ACML on ‘ix86’/‘x86_64’ Linux)
If it is mandatory (?), I should use this code:
--with-lapack="-L/path/to/libs -llapack -lcblas"
But where? I am using the standard installation of packages in R.
install.packages('knncat')
I am not sure of:
Is it mandatory to install lapack? I do have BLAS + LAPACK.
How to install a package without using install.packages()?
which are the choices I have now?
Please install the r-base-dev package, which will take care of the -dev packages for LAPACK and BLAS as well.
It was an old version of R. Even when I did upgrade, it does not fixed.
I followed this orders: from http://ubuntuforums.org/showthread.php?t=377323
sudo aptitude install r-base r-recommended
In R
install.packages('knncat')
Now it is working!