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?
Related
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
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 boot up a clean instance of R Studio. I don't save my environments and I don't use an Rprofile file. I tried both commands:
install.packages("viridis")
install.packages("viridis", dependencies = TRUE)
and I get this error:
installing source package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading Error : object ‘cividis’ is not exported by 'namespace:viridisLite' ERROR: lazy loading failed for
package ‘viridis’
removing ‘/home/stackinator/Rlibs/viridis’ Warning in install.packages : installation of package ‘viridis’ had non-zero exit status
Try the following:
if (!require("devtools")) install.packages("devtools")
devtools::install_github("sjmgarnier/viridis")
I am not sure why downloading it from CRAN didn't work, but devtools::install_github() downloads the source package from the repository rather than the bundled package that you get from CRAN with install.packages()
For more, check out this discussion from R Packages book:
http://r-pkgs.had.co.nz/package.html
I'm trying to install the development version (v. 0.8.0) of XMLSchema in R 3.2.0 on a Windows 64-bit computer.
Unfortunately, the release version (v. 0.7.0) doesn't work for the database I am trying to access.
However, when I try to install 0.8.0 from source, I get the following error:
> install.packages("XMLSchema", type="source", repos = NULL)
Installing package into ‘C:/Users/Will/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
* installing *source* package 'XMLSchema' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in .mergeMethodsTable(generic, mtable, tt, attach) :
trying to get slot "defined" from an object of a basic class ("list") with no slots
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/Will/Documents/R/win-library/3.2/XMLSchema'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\Will\Documents\R\win-library\3.2" "XMLSchema"' had status 1
Warning in install.packages :
installation of package ‘XMLSchema’ had non-zero exit status
Any thoughts or insight would be greatly appreciated.
The package worked for previous versions of R, perhaps it's a compatibility problem?
Thanks.