Cannot Install ShortRead Package
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Entering edit mode
Bob • 0
@bob-24186
Last seen 3.4 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
ShortRead • 1.6k views
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Entering edit mode

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?

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