trinity run_DE_analysis.pl Failed with error: ‘package ‘limma’ could not be loaded’

Question

[Rajesh]

Hi Experts, can someone please help me with this error while running run_DE_analysis.pl for DESeq2 analysis

Loading required package: edgeR
    Loading required package: limma
    Error: package or namespace load failed for ‘limma’:
    .onLoad failed in loadNamespace() for 'limma', details:
    call: library.dynam("limma", pkgname, libname)
    error: shared object ‘limma.dylib’ not found
    Failed with error:  ‘package ‘limma’ could not be loaded’
    In addition: Warning messages:
    1: package ‘edgeR’ was built under R version 3.6.2 
    2: package ‘limma’ was built under R version 3.6.2 
    Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install
    Execution halted
    Error, cmd: Rscript GSE123456.matrix.disease_vs_healthy.DESeq2.Rscript died with ret (256)  at run_DE_analysis.pl line 758.

the same is working on other machines but not on this perticular one. DESeq2, edgeR and limma are already installed in R and working . error is same for trinity 13.1 or 13.2.

Answer 1

[Mensur Dlakic]

It says it right there in your error message:

error: shared object ‘limma.dylib’ not found
Failed with error:  ‘package ‘limma’ could not be loaded’

and

1: package ‘edgeR’ was built under R version 3.6.2 
2: package ‘limma’ was built under R version 3.6.2 
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

It seems that you don't have limma installed properly, or at all. Also, it may be that your R is v3.5 while the two packages are for v3.6.2. Either way, you may need to re-install limma, and possibly edgeR as well.

If you know that it works on other machines, why don't you use them?

[Rajesh]

I know the error points something wrong with limma and edgeR. I tried re-installing them and it went throguh well as both working in R. Aalso tried using same version of R that is instaleld on the other machines where its working but the same error keep coming in this perticular one. I dont know why ? Ofcourse, I can use other systems but wanted to know why this is not working on this machine. I asked this question if anyone also came across this issue ?