Can't install rtracklayer on CentOS 7 and R 4 - r

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 "~"

Related

Dependency error when install ggplot in R

When I try to install ggplot with this code
install.packages("png")
install.packages("RgoogleMaps")
install.packages("ggmap")
library(ggmap)
It returns error
installing to /usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘png’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs/png.so':
dlopen(/usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs/png.so, 6): Library not loaded: #rpath/libz.1.dylib
Referenced from: /usr/local/Cellar/r/4.2.2/lib/R/library/00LOCK-png/00new/png/libs/png.so
Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/Cellar/r/4.2.2/lib/R/library/png’
Warning in install.packages :
installation of package ‘png’ had non-zero exit status
ERROR: dependency ‘png’ is not available for package ‘RgoogleMaps’
* removing ‘/usr/local/Cellar/r/4.2.2/lib/R/library/RgoogleMaps’
Warning in install.packages :
installation of package ‘RgoogleMaps’ had non-zero exit status
ERROR: dependencies ‘RgoogleMaps’, ‘png’ are not available for package ‘ggmap’
* removing ‘/usr/local/Cellar/r/4.2.2/lib/R/library/ggmap’
Warning in install.packages :
installation of package ‘ggmap’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/fd/7vyffy191_l3j6fhyqbvsn0r0000gn/T/RtmptKSXHF/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Error in library(ggmap) : there is no package called ‘ggmap’
I am installing all the dependencies that the error says are missing. By adding the install packages before installing the ggmap itself.

Cannot install vroom under R.4.0.5 on HPC node

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

Issues installing data.table in R 3.6.3 (Oct 2020)

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?

Installation issue with nflscrapR package

Having issues downloading nflscrapR. Not sure if anyone else has this issue. Output from trying to install below:
Installing package into ‘C:/Users/cciar/OneDrive/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package 'nflscrapR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package 'magrittr' was built under R version 3.6.3
Execution halted
ERROR: lazy loading failed for package 'nflscrapR'
* removing 'C:/Users/cciar/OneDrive/Documents/R/win-library/3.6/nflscrapR'
Error: Failed to install 'nflscrapR' from GitHub:
(converted from warning) installation of package ‘C:/Users/cciar/AppData/Local/Temp/Rtmp6diEQG/file5f042b671761/nflscrapR_1.8.3.tar.gz’ had non-zero exit status

r ridge package undefined symbol: regression_wrapper_function

How can I install the ridge package in R without getting the following undefined symbol error?
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘ridge’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/qwr/R/x86_64-pc-linux-gnu-library/3.4/ridge/libs/ridge.so':
/home/qwr/R/x86_64-pc-linux-gnu-library/3.4/ridge/libs/ridge.so: undefined symbol: regression_wrapper_function
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/qwr/R/x86_64-pc-linux-gnu-library/3.4/ridge’
The downloaded source packages are in
‘/tmp/Rtmp5AEXdl/downloaded_packages’
Warning message:
In install.packages("ridge") :
installation of package ‘ridge’ had non-zero exit status
Looking at the installation message, I see GSL (GNU Scientific Library) must be installed:
* installing *source* package ‘ridge’ ...
** package ‘ridge’ successfully unpacked and MD5 sums checked
checking for gsl-config... no
configure: WARNING: gsl-config not found, is GSL installed?
configure: WARNING: ridge will be installed but some functions will be unavailable
configure: creating ./config.status
Install (on Ubuntu 18.04) with sudo apt install libgsl-dev

Resources