Linux Mint package had non-zero exit status

Hi, I use Linux Mint and I have problems installing certain packages that I need for a university project. I need dplR, SPEI, treeclim, ggplot2, pointRes packages. For all packages it says "had non-zero exit status.

I would be really greatful for any help.

Thanks in advance!

You need to be more specific, select one package, show the command you are using to install it and the whole error message you are getting.

What happens if you try to install the missing dependencies? (post the whole error message)

install.packages("dplR", dependencies = TRUE )

How do I update? When I click the "update"-button in RStudio it tells me that everything is updated?

Rstudio is an IDE for the R programming language, but R is a separate software. Since Linux Mint is based on Ubuntu I think you can follow the official installation instructions for Ubuntu.

https://cran.r-project.org/bin/linux/ubuntu/

It's strange: it tells me that the latest version is already installed :thinking:

Hey, @mr.raccoon

This does not seem quite right--I suspect you are getting confirmation you have the most updated version of RStudio.

Look at the console to determine what version of R you are usingScreenshot 2020-06-14 at 10.00.05 PM

What I found confusing using R with linux is that the base- R in the main repository is far behind. You have to get Base-R and updates from a specific repo.

You may find this post helpful.

Also here from a mint forum.

Once you get the updated version of base R you can most likely update the required packages.

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

Hey I am using the"install button" and installing from repository (CRAN). So the command is e.g. "> install.packages("dplR")"

"ERROR: dependencies ‘digest’, ‘stringr’, ‘plyr’ are not available for package ‘dplR’

  • removing ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/dplR’
    Warning in install.packages :
    installation of package ‘dplR’ had non-zero exit status"
* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c colorspace.c -o colorspace.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
gcc -std=gnu99 -shared -o colorspace.so colorspace.o init.o -L/usr/lib/R/lib -lR
installing to /home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/colorspace/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘colorspace’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (colorspace)
* installing *source* package ‘fracdiff’ ...
** package ‘fracdiff’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c fdcore.c -o fdcore.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c fdgam.c -o fdgam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c fdhess.c -o fdhess.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c fdmin.c -o fdmin.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c fdsim.c -o fdsim.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c pmult.c -o pmult.o
gcc -std=gnu99 -shared -o fracdiff.so fdcore.o fdgam.o fdhess.o fdmin.o fdsim.o init.o pmult.o -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/fracdiff/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fracdiff)
ERROR: dependency ‘zoo’ is not available for package ‘lmtest’
* removing ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/lmtest’
Warning in install.packages :
  installation of package ‘lmtest’ had non-zero exit status
* installing *source* package ‘magrittr’ ...
** package ‘magrittr’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (magrittr)
* installing *source* package ‘timeDate’ ...
** package ‘timeDate’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘sample’ from package ‘base’ in package ‘timeDate’
Creating a generic function for ‘months’ from package ‘base’ in package ‘timeDate’
Creating a generic function for ‘julian’ from package ‘base’ in package ‘timeDate’
Creating a generic function for ‘getDataPart’ from package ‘methods’ in package ‘timeDate’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘timeDate’
Creating a generic function for ‘points’ from package ‘graphics’ in package ‘timeDate’
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘timeDate’
Creating a generic function for ‘abline’ from package ‘graphics’ in package ‘timeDate’
Creating a generic function for ‘frequency’ from package ‘stats’ in package ‘timeDate’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (timeDate)
ERROR: dependencies ‘quadprog’, ‘zoo’, ‘quantmod’ are not available for package ‘tseries’
* removing ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/tseries’
Warning in install.packages :
  installation of package ‘tseries’ had non-zero exit status
* installing *source* package ‘urca’ ...
** package ‘urca’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -O3 -pipe  -g  -c UnitRootMacKinnon.f -o UnitRootMacKinnon.o
gcc -std=gnu99 -shared -o urca.so UnitRootMacKinnon.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/urca/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘urca’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘urca’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (urca)
* installing *source* package ‘filehash’ ...
** package ‘filehash’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c hash.c -o hash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c lockfile.c -o lockfile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c readKeyMap.c -o readKeyMap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c sha1.c -o sha1.o
gcc -std=gnu99 -shared -o filehash.so hash.o init.o lockfile.o readKeyMap.o sha1.o -L/usr/lib/R/lib -lR
installing to /home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/filehash/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 (filehash)
* installing *source* package ‘Cairo’ ...
** package ‘Cairo’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pkg-config... /usr/bin/pkg-config
checking whether pkg-config knows about cairo... no
configure: CAIRO_LIBS is unset, attempting to guess it.
configure: CAIRO_CFLAGS=
checking if R was compiled with the RConn patch... no
checking cairo.h usability... no
checking cairo.h presence... no
checking for cairo.h... no
configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
ERROR: configuration failed for package ‘Cairo’
* removing ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/Cairo’
Warning in install.packages :
  installation of package ‘Cairo’ had non-zero exit status
* installing *source* package ‘dichromat’ ...
** package ‘dichromat’ successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (dichromat)
* installing *source* package ‘iterators’ ...
** package ‘iterators’ 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 (iterators)
* installing *source* package ‘RColorBrewer’ ...
** package ‘RColorBrewer’ 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 (RColorBrewer)
* installing *source* package ‘waveslim’ ...
** package ‘waveslim’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -O3 -pipe  -g  -c bell-p-w.f -o bell-p-w.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c dwt.c -o dwt.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c dwt2.c -o dwt2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c dwt3.c -o dwt3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c hosking.c -o hosking.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
gcc -std=gnu99 -shared -o waveslim.so bell-p-w.o dwt.o dwt2.o dwt3.o hosking.o init.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/waveslim/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (waveslim)
ERROR: dependencies ‘digest’, ‘stringr’, ‘plyr’ are not available for package ‘dplR’
* removing ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/dplR’
Warning in install.packages :
  installation of package ‘dplR’ had non-zero exit status
* installing *source* package ‘foreach’ ...
** package ‘foreach’ 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 (foreach)
ERROR: dependencies ‘ggplot2’, ‘lmtest’, ‘tseries’, ‘zoo’, ‘RcppArmadillo’ are not available for package ‘forecast’
* removing ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/forecast’
Warning in install.packages :
  installation of package ‘forecast’ had non-zero exit status
* installing *source* package ‘tikzDevice’ ...
** package ‘tikzDevice’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c tikzDevice.c -o tikzDevice.o
gcc -std=gnu99 -shared -o tikzDevice.so init.o tikzDevice.o -L/usr/lib/R/lib -lR
installing to /home/smonkey/R/x86_64-pc-linux-gnu-library/3.0/tikzDevice/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 (tikzDevice)

Installing package into ‘/home/smonkey/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependencies ‘digest’, ‘stringr’, ‘plyr’, ‘Biobase’, ‘gmp’, ‘knitr’, ‘testthat’, ‘ggplot2’, ‘zoo’, ‘RcppArmadillo’, ‘quadprog’, ‘quantmod’ are not available
also installing the dependencies ‘colorspace’, ‘fracdiff’, ‘lmtest’, ‘magrittr’, ‘timeDate’, ‘tseries’, ‘urca’, ‘filehash’, ‘Cairo’, ‘dichromat’, ‘foreach’, ‘forecast’, ‘iterators’, ‘RColorBrewer’, ‘tikzDevice’, ‘waveslim’

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--2020-06-12 19:06:31--  https://cran.rstudio.com/src/contrib/timeDate_3043.102.tar.gz
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--2020-06-12 19:06:31--  https://cran.rstudio.com/src/contrib/tseries_0.10-47.tar.gz
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--2020-06-12 19:06:34--  https://cran.rstudio.com/src/contrib/tikzDevice_0.12.3.tar.gz
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--2020-06-12 19:06:35--  https://cran.rstudio.com/src/contrib/waveslim_1.8.2.tar.gz
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--2020-06-12 19:06:35--  https://cran.rstudio.com/src/contrib/dplR_1.7.1.tar.gz
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The R version you are using is too old and some of the package dependencies are not available for it. You would need to update your R version on order to install these packages (current version 4.0.1).