Cannot Install ShortRead Package
0
0
Entering edit mode
Bob • 0
@bob-24186
Last seen 22 months 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 • 660 views
ADD COMMENT
0
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?

ADD REPLY

Login before adding your answer.

Traffic: 469 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6