I need help installing a package "DESeq2" having BiocManager issues

[price793]

Hi R community,

I am new to R and have been having issues installing the "DESeq2" package that I need to do a particular data transformation. I have tried many things and I would like help. I've tried posting in the BioConducter blogs but I am out of messages for the day. Essentially, I seem to be having problems with installing "GenomeInfoDbData" and get stuck at a non-zero exit status. I've been reading some of the posts here and from my understanding I should be able to install from a source that does not need compilation to get access to an older version of the package but it still reports a non-zero exit status. Can you please help me? I've been stuck on this problem for a long time. ):

The downloaded source packages are in
‘/private/var/folders/yq/0npyx_c53h11vckppmcv5vmc0000gn/T/Rtmpuvn0DW/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘GenomeInfoDbData’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘backports’ had non-zero exit status

[technocrat]

First,

install.packages("backport")

You will be offered a choice to install v 1.1,10 from source. Choose Yes. If it fails, required operating system facilities are missing. Try again and choose No.

Following successful installation of backports

BiocManager::install("DESeq2")

will succeed under

sessionInfo()
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
...

[price793]

Hi technocrat,

I appreciate your help! So, I tried doing those things and installed the backports. Should I update my OS to Catalina?

library(DESeq2)
Loading required package: GenomicRanges
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
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Sierra 10.12.6

[technocrat]

@price793

there is no package called ‘GenomeInfoDbData’

indicates another missing dependency to be installed, probably by

BiocManager::install("GenomeInfoDbData")

macOS, R packages and RStudio should be kept roughly synchronized. It is usually not necessary to be at the latest point release, but problems begin accumuating as one or more installed versions begin lagging by a major release.

In addition, macOS suffers from a default configuration that does not include tools required to compile packages from source, when that is necessary. (Most packages are available in binary form, but not always).

[Tulip]

I am facing the same problem. I tried a lot of things, but did not find a solution.

BiocManager::install("GenomeInfoDbData")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'GenomeInfoDbData'

package ‘GenomeInfoDbData’ is available as a source package but not as a binary

Warning message:
package ‘GenomeInfoDbData’ is not available (as a binary package for R version 4.0.2)

[price793]

Hi Tulip,

I figured out the problem. I was using an out of date operating system for R and it wouldn't install DESeq2 which was my main objective. So, maybe try updating your operating system?

Best