Installing package

Question

I come across this problem when I install the package

"TxDb.Hsapiens.UCSC.hg19.knownGene" from Bioclite on RStudio v.1.1442. Below is the error message: Warning messages: /TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz' had status 3 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status

I also tried to install this package, but it did not work either: Warning in install.packages : package ‘parallel’ is not available (for R version 3.4.3) Warning in install.packages : package ‘parallel’ is a base package, and should not be updated

I do not understand what the warnings mean and can someone please help me with resolving this issue?

Thank you.

Did you use the "Tools>Install_packages" route, or the "biocLite(...)" route? — Russ Hyde
@anyanwu: I tried but it did not work on my RStudio version. Thank you. — Ashley
Could you confirm that you have installed the dependencies: AnnotationDbi / GenomicFeatures — Russ Hyde

Russ Hyde Russ Hyde · Accepted Answer · 2018-03-22T18:59:59

Some further details would be very helpful - especially the code that you actually used. What OS are you working on? Is this a fresh install of R? Have you previously had TxDB.... installed? Are you working in a conda environment or similar? Why did you download the gzipped version of the package?

In a fresh R-3.4.3 environment on Ubuntu I get the following

source("http://www.bioconductor.org/biocLite.R")

## installing source BiocInstaller blah blah success

biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RMySQL’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status

This suggests that if I wanted to install TxDB... I'd have to get RMySQL installed first, and then GenomicFeatures and then ....

Could you post all the code you used and all the contents of the warning messages that you received, please.

Installing package

1 Answers