I'm running RStudio Server and am unable to install the zoo package. The error message I get is as follows:
Installing package(s) into ‘/home/tsajid/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://mirrors.nics.utk.edu/cran/src/contrib/zoo_1.7-9.tar.gz'
Content type 'application/x-gzip' length 807084 bytes (788 Kb)
opened URL
==================================================
downloaded 788 Kb
** installing source package ‘zoo’ ...
** package ‘zoo’ successfully unpacked and MD5 sums checked
** libs
sh: make: command not found
ERROR: compilation failed for package ‘zoo’
** removing ‘/home/tsajid/R/library/zoo’
Warning in install.packages :
installation of package ‘zoo’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpsKlJWz/downloaded_packages’
I tried installing the package archive file but I get an identical error message.
Session info:
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] svMisc_0.9-65
loaded via a namespace (and not attached):
[1] tools_2.15.1
It states it pretty clearly:
sh: make: command not found
So please do install the Red Hat equivalent of the Debian / Ubuntu command
sudo apt-get install r-base-dev
which via its dependence on build-essential also installs make, gcc etc pp
Related
I'm currently trying to use readFastq with the ShortRead library. I have specified the version of Bioconductor I need (3.14) in order to run it in R version 4.1 (which is the one I'm currently using). I keep getting an error message saying:
> library(ShortRead)
Error in library(Shortread) : there is no package called 'ShortRead'
and also:
ln: failed to create symbolic link 'libhts.so.2': Operation not supported
make: *** [Makevars:28: populate-usrlib-dir] Error 1
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘Rhtslib’ are not available for package ‘ShortRead’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/ShortRead’
and
ERROR: configuration failed for package ‘textshaping’
* removing ‘/opt/conda/envs/r/lib/R/library/textshaping’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/textshaping’
* installing *source* package ‘ragg’ ...
** package ‘ragg’ successfully unpacked and MD5 sums checked
** using staged installation
and lastly
ERROR: configuration failed for package ‘ragg’
* removing ‘/opt/conda/envs/r/lib/R/library/ragg’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/ragg’
The downloaded source packages are in
‘/tmp/RtmpgByRyT/downloaded_packages’
I would really appreciate som help with troubleshooting this or a "smarter" way to convert fastq.gz files to fasta files
The commands I've run so far are:
#Installing ShortRead package containing the readFastq function
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="3.14")
BiocManager::install("GenomeInfoDbData")
BiocManager::install("GenomeInfoDb")
BiocManager::install("ShortRead")
#Loading the library
library(ShortRead)
Some extra session information:
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS/LAPACK: /opt/conda/envs/r/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.19
loaded via a namespace (and not attached):
[1] compiler_4.1.1 fastmap_1.1.0 cli_3.4.1 htmltools_0.5.3 tools_4.1.1
[6] rstudioapi_0.14 yaml_2.3.6 rmarkdown_2.17 knitr_1.40 xfun_0.34
[11] digest_0.6.30 rlang_1.0.6 evaluate_0.17
I do not understand why it won't install. I would it expect it to work when I have made sure to use the correct version
Every package I try to install is met with the following error:
* installing *source* package ‘dichromat’ ...
** package ‘dichromat’ successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘dichromat’
finding HTML links ... done
colorschemes html
dalton html
Error: invalid regular expression '^[[:blank:]]*
'
* removing ‘/newhome/vdp5/R/x86_64-redhat-linux-gnu-library/3.3/dichromat’
ERROR: dependency ‘dichromat’ is not available for package ‘scales’
* removing ‘/newhome/vdp5/R/x86_64-redhat-linux-gnu-library/3.3/scales’
The downloaded source packages are in
‘/tmp/RtmpVXl3tg/downloaded_packages’
Warning messages:
1: In install.packages("scales") :
installation of package ‘dichromat’ had non-zero exit status
2: In install.packages("scales") :
installation of package ‘scales’ had non-zero exit status
I have no idea why this installation keeps failing and have been unable to make any progress in potentially hacking together a solution.
My session info is as follows:
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
I am trying to install stringi package in R, but the installation never finishes. After the download and some compilation, I get the following message:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi/libs/stringi.so':
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi/libs/stringi.so)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi’
The downloaded source packages are in
‘/tmp/RtmpT5KQVP/downloaded_packages’
Warning message:
In install.packages("stringi") :
installation of package ‘stringi’ had non-zero exit status
I searched the internet and I couldn't understand what this error message means. If it helps, this is my sessionInfo():
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.3.1
I solved my problem installing gcc 4.9.2. To do so, I ran
$ sudo yum install devtoolset-3-gcc-c++
$ sudo yum install devtoolset-3-gcc-gfortran
$ scl enable devtoolset-3 bash
in the shell. The first two commands install gcc and gfortran. The last one makes gcc 4.9.2 the standard compiler in the system. After that, I opened R and ran install.packages("stringi") to have my problem solved.
I have just initiated a EC2 server on AWS and I'm trying to install a package from
github called 'krose/skm'. The package is installed without any issues on Windows, but not on Ubuntu. All dependencies are installed. I can't figure out why it can install on Windows, but not Ubuntu.
library(devtools)
install_github('krose/skm')
And the result of running the code above is:
Downloading GitHub repo krose/skm#master
from URL https://api.github.com/repos/krose/skm/zipball/master
Installing skm
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/RtmpxJg8N7/devtools1b887e511e96/krose-skm-059766b' \
--library='/usr/local/lib/R/site-library' --install-tests
* installing *source* package ‘skm’ ...
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in namespaceExport(ns, exports) :
undefined exports: skm_umm_stations, skm_ummquery, skm_webquery
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/skm’
Error: Command failed (1)
The functions are documented using Roxygen2 and are exported. The functions are not assigned using <<-.
Here is my sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.11.1
loaded via a namespace (and not attached):
[1] httr_1.1.0 R6_2.1.2 tools_3.2.5 withr_1.0.1 curl_0.9.7
[6] memoise_1.0.0 git2r_0.14.0 digest_0.6.9
I don't have much experience with Ubuntu.
UPDATE: The R CMD check has the following two notes:
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
'README.Rmd'
The R directory in the package was misnamed as r. Windows didn't pick up on the difference, since it is more forgiving about differences in case for file and directory names.
I want to use Feature Selection with the Caret R Package, but I can't install it on my linux machine. I've tried various things, I've also used dependencies=TRUE inside install.packages with no results. Any help?
Here is the log:
Warning: dependency 'car' is not available
trying URL 'http://cran.rstudio.com/src/contrib/caret_6.0-52.tar.gz'
Content type 'application/x-gzip' length 3665293 bytes (3.5 Mb)
opened URL
==================================================
downloaded 3.5 Mb
ERROR: dependency 'car' is not available for package 'caret'
* removing '/usr/lib64/R/library/caret'
The downloaded source packages are in
'/tmp/RtmpKfvgyR/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("caret") :
installation of package âcaretâ had non-zero exit status
>
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
UPDATE:
I've upgraded R to version 3.2.1 and now I can install caret package. Just sudo yum install R and it was solved.