Comments (2)
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?
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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!
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Related Issues (20)
- eror in data frame HOT 9
- LEAstructure error HOT 4
- Problem creating RAW file HOT 2
- problems running getpackages HOT 1
- Issue with z scores for d statistics HOT 10
- Error in findstructure() HOT 3
- ERROR: duplicate sample names found in input data (PED file) HOT 2
- mergepop() issue HOT 2
- error with output for dapc_ascore in file dapc.K.#.#.scatter.dapc.WITH_prior_popinfo.axis1vs2.dc_score.txt HOT 4
- optim.a.score n.sim arg HOT 4
- Return of a problem you solved for someone previously HOT 3
- Error with calcdiversity output HOT 9
- Can't figure out how to use latitude/longitude because I need to use genlight format to import my data HOT 2
- OutFLANK problems so selectionanalysis() fails
- Possible new option? HOT 2
- unable to add Bayescan output HOT 13
- Trying to exclude some populations (which I did before). Error says to send it to you. HOT 4
- using the selectionanalyses function HOT 1
- calckinship() and pairwise_relatedenss being recalculated HOT 1
- mapping issues HOT 1
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