To install another package that depends on vroom (which failed) on a HPC node, I sought to install vroom manually.
I tried to install the package manually but it fails too:
My code:
install.packages("vroom")
error message:
installing to /home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-vroom/00new/vroom/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘vroom’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-vroom/00new/vroom/libs/vroom.so':
/home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-vroom/00new/vroom/libs/vroom.so: undefined symbol: __cxa_init_primary_exception
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/leuph1/R/x86_64-pc-linux-gnu-library/4.0/vroom’
Warning in install.packages :
installation of package ‘vroom’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpgPcp9Y/downloaded_packages’
I have tried under different R versions (3.5.3 up to 4.1.1) but keep having the same issue no matter what version I chose.
I have also deleted any 00LOCK-"package-name" folder that might have arisen in the process in the corresponding R Version package folder, but to no avail.
Can anybody help me out here?
Many thanks in advance,
Philibertus88
Related
I'm trying to install a package on Bioconductor called "Herper" and it requires "hdf5r" to be updated. I'm trying to update using compilation to get the most recent version of this package. Previously, I had issues with finding the hdf5 library but was able to rectify this by first installing hdf5 using homebrew and then using the following code to specify the location of the hdf5 library.
install.packages("hdf5r", configure.args = "--with-hdf5=/opt/homebrew/Cellar/hdf5/1.12.2_2/bin/h5cc")
Now I'm getting a new error where R is trying to find the object 'hdf5r.so'.
Here is where I believe things start going wrong:
ld: warning: ignoring file /opt/homebrew/Cellar/hdf5/1.12.2_2/lib/libhdf5_hl.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
ld: warning: ignoring file /opt/homebrew/Cellar/hdf5/1.12.2_2/lib/libhdf5.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-hdf5r/00new/hdf5r/libs
** 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 from temporary location
Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-hdf5r/00new/hdf5r/libs/hdf5r.so, 0x0006): symbol not found in flat namespace (_H5P_CLS_ATTRIBUTE_CREATE_ID_g)
Error: loading failed
Execution halted
ERROR: loading failed
I'm quite new to coding, so I believe the 00LOCK folders are temporary folders? Because I cannot find the path that R is searching for. Let me know if you guys have any solutions to this!
Cheers,
G
I'm using a Mac with OS Sierra 10.12.5. I'm having trouble with installing the R package "data.table," including if I try to install via install.packages("Hmisc"), or install.packages("data.table"). Both result in:
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-data.table/00new/data.table/libs
** 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 from temporary location
Error: package or namespace load failed for ‘data.table’ in library.dynam(lib, package, package.lib):
shared object ‘datatable.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/data.table’
The downloaded source packages are in
‘/private/var/folders/bl/lgd7_j2j087f24tcly84xg580000gn/T/RtmpbM5EaD/downloaded_packages’
Warning message:
In install.packages("data.table") :
installation of package ‘data.table’ had non-zero exit status
I then tried installing directly from the .zip at: https://github.com/Rdatatable/data.table, but got the following "not available for R 3.6.3" message:
> install.packages("~/Downloads/data.table-master.zip")
Warning message:
package ‘~/Downloads/data.table-master.zip’ is not available (for R version 3.6.3)
I tried the approaches in this thread, but none worked :\ : Problems installing data.table for R
Any advice for what I can try next, or where I can access a version of data.table specifically for R 3.6.3?
I have tried installing the rtracklayer package using Bioconductor on R 4.0.2 and CentOS 7 without success. This is the error that I get:
installing to ~/bin/R/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '~/bin/R/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/rtracklayer.so':
~/bin/R/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs/rtracklayer.so: undefined symbol: CRYPTO_set_locking_callback
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘~/bin/R/lib64/R/library/rtracklayer’
The downloaded source packages are in
‘/tmp/Rtmpet2cyn/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
installation of package ‘rtracklayer’ had non-zero exit status
I haven't been able to fix this. Note: I've changed the absolute address of my home folder to "~"
I want to install a package that is not found in CRAN.
Below is a downloadlink to the package.
The package makes use of JAGS, of which i have the 64 bit 4.3.0 version of.
rjags and r2jags packages are installed. Rtools is connected to the pathway. I checked this using
Sys.which("make")
## "C:\\rtools40\\usr\\bin\\make.exe"
Connection to path was done with devtools from this Stacklink:
How to add Rtools\bin to the system path in R
I use the following code to install the downloaded .tar.gz package:
install.packages("C:/Program Files/R/R-3.6.3/Liszt_0.8-5_1.tar.gz", repos=NULL,
type="source")
The package won't installl, instead i get the following error:
* installing *source* package 'Liszt' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Liszt'
finding HTML links ... done
A3ModelFun html
A5ModelFun html
Caterpillar html
LL html
Liszt-package html
extract html
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'rjags':
.onLoad failed in loadNamespace() for 'rjags', details:
call: fun(libname, pkgname)
error: Failed to locate any version of JAGS version 4
The rjags package is just an interface to the JAGS library
Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
http://www.sourceforge.net/projects/mcmc-jags/files
Error : package 'rjags' could not be loaded
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/Sneve/Documents/R/win-library/3.6/Liszt'
Warning in install.packages :
installation of package ‘C:/PROGRA~1/R/R-36~1.3/Liszt_0.8-5_1.tar.gz’ had non-zero exit status
I am trying for a while no, but no success. Any help is much appreciated.
Website providing the package:
http://www.possinghamlab.org/2016-05-30-04-33-10/list-length-analysis.html
package is available here:
http://www.possinghamlab.org/images/LLA/Liszt_0.8-5_1.tar.gz
I installed the 64 Bit version of JAGS. Appearently, the package needs both the 32 and the 64 bit version installed on the PC to be able to work. After i installed also the 32 bit version of JAGS, package installed with no problem.
I'm running on Ubuntu 16.04 (on a Lenovo ThinkPak T450). I have installed R version 3.4.1, installed by following the instructions here via Rbloggers.
From here, I would like to start installing packages, but if I run R from the command line without root privileges, I cannot access a CRAN mirror. That is, when I run install.packages('dplyr') (or any install.packages('blah')) I get the following error
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/opt/anaconda1anaconda2anaconda3/lib/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.18/library ./tcl8.5.18/library
With that error, no CRAN mirror dialog box appears and hence no installation of packages. Note: this error does not happen when I start R with root privileges (i.e., start via > sudo R), but I do not want to install packages as root.
Thanks in advance for any help you can send my way!
Edit: Specifying the repo also results in error (in the file paths below, I replaced my user-name with user-name).
E.g.: install.packages('Rcpp',repos='http://cran.us.r-project.org') terminates with:
installing to /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘Rcpp’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so':
/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEED1Ev
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp’
E.g., install.packages('dplyr',repos='http://cran.us.r-project.org') terminates with:
installing to /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp/libs/bindrcpp.so':
/home/user-name/anaconda3/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp/libs/bindrcpp.so)
ERROR: lazy loading failed for package ‘dplyr’
* removing ‘/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/dplyr’
As pointed out by DirkEddelbuettel in the comments, the issue was a mixing of Anaconda and R. To fix this problem:
I uninstalled the R packages from Anaconda by first looking at > conda list and realizing that the package was r-base; hence running > conda remove r-base.
Next, by looking at the output of > which R, it was clear that we were still trying to execute from the ../anaconda3/bin/.. directory. I suspect there is a quick way to change this via an export or bashrc amendment (or something similar), but for me, the quickest work-around was to run > sudo apt-get install r-base r-base-dev, which took all of 0.2 seconds as they were already installed, but it did affect the directory which the system looks in to the appropriate one, for me this is /usr/bin/R/.
From here I've been able to install everything I've needed.
Note: Thinking back, I suspect the "mixing" happened when I installed rpy2 via conda.