PCAdapt do_pcadapt = FALSE not working in getpackages about sambar

[mennodejong1986]

Hi Maeva, thanks for the positive feedback! Yes, for some reason the getpackages function behaves problematic for PCadapt and other bioconductor packages. Before I look into this, could you confirm that you 'told' SambaR not to attempt to install 'PCadapt', by setting within the mypackageslist.txt file the flags 'do_install' and 'do_load' to FALSE?

Also, and importantly, SambaR needs the old PCadapt version 4.1.0. The reason is that a crucial utility of PCadapt has been deprecated in later versions, and as a result the selectionanalyses() function will not run properly if using a more recent PCadapt version. Are you sure you want to install the latest PCadapt version?

[MaevaTecher]

Hi Menno,

Thanks for your prompt reply and I understand now the interest of keeping the previous version of 'pcadapt'. After following your suggestion with mypackageslist.txt, I had no issues with this error when ignoring the package for downstream analysis.

However, I figured out that the main issue was not with your code but with my version of gfortran which kept popping up when I tried to install the old version 4.1.0 of pcadapt. So in case, someone else has the same issue as me, I just follow this https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ and it solved it

Thanks again for the help!