include your problematic code here with any corresponding output

Question

Cannot install ShortRead package

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Bob • 0

@bob-24186

Last seen 3.4 years ago

Enter the body of text here

Code should be placed in three backticks as shown below

library(ShortRead)

<h2>I tried as well downloading GenomeInfoDb</h2>

include your problematic code here with any corresponding output

please also include the results of running the following in an R session

sessionInfo( )


Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded

ShortRead • 2.2k views

ADD COMMENT • link updated 3.4 years ago by Martin Morgan 25k • written 3.4 years ago by Bob • 0

score 0 · Answer 1 · 2020-11-19

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Martin Morgan 25k

@martin-morgan-1513

Last seen 2 days ago

United States

Start by ensuring that you are using the current version of Bioconductor, and that the packages are current

BiocManager::version()  # should be 3.12
BiocManager::valid()    # should be TRUE

Then install GenomeInfoDbData

BiocManager::install("GenomeInfoDbData")

and finally GenomeInfoDb

BiocManager::install("GenomeInfoDb")

ADD COMMENT • link 3.4 years ago Martin Morgan 25k

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Hi. Yes I am using the current version of Bioconductor. Also "GenomeInfoData" and "GenomeInfoDb" were loaded.

ADD REPLY • link 3.4 years ago Bob • 0

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Can you help then to debug the problem that you report

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded

? What is the output of BiocManager::install("GenomeInfoDbData")? I have

> BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.13 (BiocManager 1.30.10), R Under development (unstable)
  (2020-11-13 r79426)
Installing package(s) 'GenomeInfoDbData'
trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/GenomeInfoDbData_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10673545 bytes (10.2 MB)
==================================================
downloaded 10.2 MB

* installing *source* package 'GenomeInfoDbData' ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

The downloaded source packages are in
    '/private/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T/RtmpCu24rC/downloaded_packages'
>

ADD REPLY • link 3.4 years ago Martin Morgan 25k

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I was successfully reloaded the "GenomeInfoDbData" but still I'm seeing the same message for "ShortRead"

ADD REPLY • link 3.4 years ago Bob • 0

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Please copy and paste the command the you execute, and the error that you see. Be sure to do these commands in a new R session, with no other R sessions open.

ADD REPLY • link 3.4 years ago Martin Morgan 25k

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I tried your feedback before. But this time, in the R console itself.

BiocManager::version()
[1] '3.12'
BiocManager::valid()
[2] TRUE

BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'GenomeInfoDbData'
trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GenomeInfoDbData_1.2.4.tar.gz'
Content type 'application/x-gzip' length 10673545 bytes (10.2 MB)

==================================================
downloaded 10.2 MB

* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

The downloaded source packages are in
    ‘/tmp/RtmpgJPpDc/downloaded_packages’
Installation path not writeable, unable to update packages: foreign, spatial

And then I tried to install ShortRead, but still I'm seeing this type of message:

BiocManager::install("ShortRead")
.
.
.
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

ADD REPLY • link 3.4 years ago Bob • 0

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So this is now a different set of errors. Look at the first error

1: In install.packages(...) :
installation of package ‘Rhtslib’ had non-zero exit status

and see why that failed, perhaps trying

BiocManager::install("Rhtslib")

ADD REPLY • link 3.4 years ago Martin Morgan 25k