I have installed R-3.6.1 on 64 bit slackware v14.2-current. I am trying to install an R library, rgdal. I have tried the installation from within R with
install.packages("rgdal")
and
The installation fails with the error:
...
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/user/R/x86_64-slackware-linux-gnu-library/3.6/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
libgdal.so.20: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/user/R/x86_64-slackware-linux-gnu-library/3.6/rgdal’
My GDAL installation:
bash-5.0$ gdalinfo --version
GDAL 2.4.4, released 2020/01/08
Search for libgdal:
bash-5.0$ locate libgdal.so
/usr/local/lib/libgdal.so
/usr/local/lib/libgdal.so.26
/usr/local/lib/libgdal.so.26.0.1
I tried
install.packages('rgdal', type = "source", configure.args=c('--with-libgdal=/usr/local/lib/libgdal.so.26'))
not having any idea what would happen. It failed with the same error message as above.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-slackware-linux-gnu (64-bit)
Running under: Slackware 14.2 x86_64 (post 14.2 -current)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[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] compiler_3.6.1 tools_3.6.1 tcltk_3.6.1
R/rgdal is searching for libgdal.so.20 and I have .26, but no .20. I don't know how to, and if I should, point the install.packages() function at v.26. Will it work if the script points at .26? How do I get the script to point to the newer version of libgdal.so?
EDIT-After the comment from Roman Luštrik, I copied
cp /usr/local/lib/libgdal.so.26 /usr/lib64/
cp /usr/local/lib/libgdal.so /usr/lib64/
Then tried install.packages("rgdal") again. It failed again with a similar error message as first, except now it was missing "libproj.so.15". Thus, repeated steps:
cp /usr/local/lib/libproj.so /usr/lib64
cp /usr/local/lib/libproj.so.15 /usr/lib64
Tried install.packages("rgdal") again. This time the error was
Error: proj/epsg not found
Either install missing proj support files, for example
the proj-nad and proj-epsg RPMs on systems using RPMs,
or if installed but not autodetected, set PROJ_LIB to the
correct path, and if need be use the --with-proj-share=
configure argument.
bash-5.0# export PROJ_LIB=/usr/share/proj
bash-5.0# echo $PROJ_LIB
/usr/share/proj
Try install.packages("rgdal") again. Now the error is:
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/user/R/x86_64-slackware-linux-gnu-library/3.6/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
/home/user/R/x86_64-slackware-linux-gnu-library/3.6/00LOCK-rgdal/00new/rgdal/libs/rgdal.so:
undefined symbol: pj_get_ellps_ref
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'm having problem installing "Rcurl" in Rstudio on opensuse 15.2. I have installed Rstudio from the OS repository, I have been searching for similar questions and answers, and found this other question which I think it's the closest one to mine but in Ubuntu. Following some suggestions I didn't get to solve the problem in my case. Here is the error I get:
Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/alcides/R/x86_64-suse-linux-gnu-library/3.5/RCurl/libs/RCurl.so':
libicui18n.so.58: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/username/R/x86_64-suse-linux-gnu-library/3.5/RCurl’
Warning in install.packages :
installation of package ‘RCurl’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpKXseTK/downloaded_packages’
This is my session info
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
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] compiler_3.5.0 tools_3.5.0
Thanks
I reproduced the error and at first I couldn't install RCurl. The way I solved is by installing:
sudo zypper install libcurl-devel
And then from R
install.packages ("RCurl")
Among the packages available for Leap 15.2 is also R-RCurl-1.95_4.11-lp152.6.7.x86_64.rpm, but it is for R 4.0.2, not 3.5 like the one you use.
I am pretty desperate to install.packages("devtools").
However it allways fails with this error
Error: .onLoad failed in loadNamespace() for 'pkgload', details:
call: readRDS(nsInfoFilePath)
error: error reading from connection
Execution halted
ERROR: lazy loading failed for package ‘devtools’
* removing ‘/home/bjoern/R/x86_64-pc-linux-gnu-library/3.6/devtools’
Things I tried to fix this:
Add the dependencies = T argument
Following a suggestion by hadley wickham on github -> update rlang package
Try to run install.packages("pkgload") resulting in nearly exactly the same error (see below)
Completely removing R and reinstalling it
Additionally installing package following packages:
r-base-dev
r-cran-devtools
r-recommended
Updated all packages update.packages(ask = FALSE, checkBuilt = TRUE)
Error of install.packages("pkgload")
Error: package or namespace load failed for ‘pkgload’:
.onLoad failed in loadNamespace() for 'pkgload', details:
call: readRDS(nsInfoFilePath)
error: error reading from connection
Error: loading failed
Execution halted
ERROR: loading failed
I digged even deeper to the pkgload (which at least I hope is the only reason for the problem). I will check if manually (re)installing all imports and suggests from the CRAN page of pkgload does solve it.
Imports: desc, methods, pkgbuild, rlang, rprojroot, rstudioapi,
utils, withr Suggests: bitops, covr, Rcpp, testthat
My sessionInfo() output:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3
I still refuse to belief that it is impossibe to install devtools on ubuntu20
However at this point I take any straw
Solution Edit:
In short what fixed the issue for me was installing testthat package before. Thanks to comment by rui-barradas
install.packages("testthat")
install.packages("pkgload")
install.packages("devtools")
I am also on Ubuntu 20.04 but running R 4.0.0.
When trying to install a package, if it depends on another that was installed prior to R 4.0.0 I get an error message and the installation fails. This happens even if I set dependencies = TRUE in the call to install.packages.
Example: The command was
install.packages('pkgload')
I omit the first output lines, saying that the file was downloaded. Then, the relevant part.
installing source package ‘pkgload’ ...
** package ‘rcmdcheck’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading Error: package ‘testthat’ was installed before R 4.0.0: please re-install it
Execution halted ERROR: lazy loading failed for package ‘pkgload’
removing ‘/usr/local/lib/R/site-library/pkgload’
restoring previous ‘/usr/local/lib/R/site-library/pkgload’ Warning in install.packages : installation of package ‘pkgload’ had
non-zero exit status The downloaded source packages are in
‘/tmp/RtmpVxpbs0/downloaded_packages’
Correct way.
The right way of installing package pkgload was to run the sequence
install.packages('testthat')
install.packages('pkgload')
and the problem was solved.
Note that with other packages, it already happened to see this be a recursive issue. Imagine that package testthat depended (which it does not) on another package installed prior to R 4.0.0.
Annoying but solvable.
sessionInfo()
#R version 4.0.0 (2020-04-24)
#Platform: x86_64-pc-linux-gnu (64-bit)
#Running under: Ubuntu 20.04 LTS
#
#Matrix products: default
#BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#
#locale:
# [1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C
#[3] LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8
# [5] LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8
# [7] LC_PAPER=pt_PT.UTF-8 LC_NAME=C
# [9] LC_ADDRESS=C LC_TELEPHONE=C
#[11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C
#
#attached base packages:
#[1] stats graphics grDevices utils datasets
#[6] methods base
#
#other attached packages:
#[1] rvest_0.3.5 xml2_1.3.2 data.table_1.12.8
#
#loaded via a namespace (and not attached):
I had the same problems, and the solution was, at least in my case, Ubuntu 20.04.1 LTS (Focal Fossa) + R 4.0.2:
First (from terminal), install:
Step 1: sudo apt-get update -y
Step 2: sudo apt-get install -y libxml2-dev
Then from RStudio (setRepositories first, and choose 8 repositories) and install both packages:
Install xml2 package
install devtools
And works for me.
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.