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Bob
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0
@bob-24186
Last seen 4.2 years ago
I need help in installing ShortRead package from Bioconductor.
My R is version 4.0.3 and my Bioconductor is the latest version.
# Entered input code
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ShortRead")
# Here is the output
sessionInfo( )
The downloaded source packages are in
‘/tmp/RtmptnxMoF/downloaded_packages’
Installation path not writeable, unable to update packages: foreign, spatial
Warning messages:
1: In install.packages(...) :
installation of package ‘Rhtslib’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘Rsamtools’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘GenomicAlignments’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘ShortRead’ had non-zero exit status
I believe Rhtslib might have system dependencies that may need to be installed? Have you checked to ensure those are on your system so
BiocManager::install('Rhtslib')
installs correctly?