Error: package or namespace load failed for 'DESeq2' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so, 0x0006): Library not loaded: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib'
Referenced from: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so'
Reason: tried: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)
1. Install xcode.
2. Indtal XQuarz
Follow the instruction on this website to install Deseq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
This code is important:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
Please post more details if it doesn't work.
Related
I installed ChemmineR and ChemmineOB on my MacOSX (MaxOS Ventura; R version 4.2.1) and got this:
library(ChemmineOB)
Error: package or namespace load failed for ‘ChemmineOB’:
.onLoad failed in loadNamespace() for 'ChemmineOB', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so, 0x000A): Library not loaded: /usr/local/opt/open-babel/lib/libopenbabel.7.dylib
Referenced from: <77D86F2D-1FC2-3CDF-81D4-73A54E882F99> /Library/Frameworks/R.framework/Versions/4.2/Resources/library/ChemmineOB/libs/ChemmineOB.so
Reason: tried: '/usr/local/opt/open-babel/lib/libopenbabel.7.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/opt/open-babel/lib/libopenbabel.7.dylib' (no such file), '/usr/local/opt/open-babel/lib/libopenbabel.7.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libopenbabel.7.dylib' (no such file), '/Users/hanyan/l
I have a binder set up that makes use of highcharter. The package is installed, the system can find it and it is up to date. But when trying to attach it with library I get this:
> library(highcharter)
Error: package or namespace load failed for ‘highcharter’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/srv/rlibs/igraph/libs/igraph.so':
libglpk.so.40: cannot open shared object file: No such file or directory
I noted the mention of igraph, so I tried attaching that, but get the same error:
> library(igraph)
Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/srv/rlibs/igraph/libs/igraph.so':
libglpk.so.40: cannot open shared object file: No such file or directory
I've tried installing the latest dev version from github. The result of this was an error:
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/tmp/RtmpK0dUBK/Rinst15a72b8aab6/00LOCK-igraph/00new/igraph/libs/igraph.so':
libopenblas.so.0: cannot open shared object file: No such file or directory
Error: loading failed
The binder system info is:
> Sys.info()
sysname
"Linux"
release
"5.4.129+"
version
"#1 SMP Wed Aug 18 19:58:18 PDT 2021"
nodename
"jupyter-nhsbsa-2ddata-2dana-2dffee-2dand-2dcoding-2d5y1715cc"
machine
"x86_64"
After several hours of Googling I've reached the limit of what I can do to troubleshoot this, any help appreciated!
Resolved by adding libglpk-dev to the apt.txt file. It is strange tho, as this did not used to be needed and it worked.
I get this error when starting the export package in R. It seems to download successfully, but when library(export) is run, I get this message:
Error: package or namespace load failed for ‘export’ in dyn.load(file,
DLLpath = DLLpath, ...): unable to load shared object
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdtools/libs/gdtools.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdtools/libs/gdtools.so,
6): Library not loaded: /opt/X11/lib/libcairo.2.dylib Referenced
from:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdtools/libs/gdtools.so
Reason: image not found
Thanks for your help!
I'm trying to load a package I have installed via Bioconductor (using BiocLite()) as I have done with many other similar packages from the same source. However I get this error:
[Error: package or namespace load failed for 'GenomicFeatures' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/mario/Library/R/3.4/library/rtracklayer/libs/rtracklayer.so':
dlopen(/Users/mario/Library/R/3.4/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
Referenced from: /Users/mario/Library/R/3.4/library/rtracklayer/libs/rtracklayer.so
Reason: image not found]
If I try to install and load library rtracklayer I get the same message
I've tried reading to answers for similar questions on the site but I still can't figure out what the problem is.
Any suggestions?
I use Rblpapi package on a PC at work. I've tried to install it on my Mac at home, however, I get the below error. I'm not sure what the problem is... all other packages work. Any suggestions?
library(Rblpapi)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/wg/Library/R/3.3/library/Rblpapi/libs/Rblpapi.so':
dlopen(/Users/wg/Library/R/3.3/library/Rblpapi/libs/Rblpapi.so, 6): Library not loaded: #rpath/libblpapi3_64.so
Referenced from: /Users/wg/Library/R/3.3/library/Rblpapi/libs/Rblpapi.so
Reason: image not found
Error: package or namespace load failed for ‘Rblpapi’