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
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
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.
Trying to install package "caret" on R 3.1.0 (Ubuntu 14.04.01 LTS) and running into a build error.
> install.packages('caret')
[...]
* installing *source* package ‘BradleyTerry2’ ...
** package ‘BradleyTerry2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object ‘brglm’ is not exported by 'namespace:brglm'
ERROR: lazy loading failed for package ‘BradleyTerry2’
* removing ‘/home/br00t/R/x86_64-pc-linux-gnu-library/3.1/BradleyTerry2’
Warning in install.packages :
installation of package ‘BradleyTerry2’ had non-zero exit status
ERROR: dependency ‘BradleyTerry2’ is not available for package ‘caret’
* removing ‘/home/br00t/R/x86_64-pc-linux-gnu-library/3.1/caret’
Warning in install.packages :
installation of package ‘caret’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp7pWmvr/downloaded_packages’
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sp_1.0-16
loaded via a namespace (and not attached):
[1] grid_3.1.0 lattice_0.20-29 tools_3.1.0
Wasn't able to find anything helpful on the interwebs. Not sure if this is an issue with the BradleyTerry2 package or brglm... help?
Thanks,
br00t
If you are running a version of the brglm package greater than 0.5-9, uninstall and install brglm package version 0.5-9
I was able to get over the issue too by installing the dependencies. You may want to select your answer as the right one.
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