Package deprecated? Thanks

[grimmem1]

devtools::install_github("joelnitta/gbfetch") Downloading GitHub repo joelnitta/gbfetch@HEAD tar (child): gzip: Cannot exec: No such file or directory tar (child): Error is not recoverable: exiting now /bin/tar: Child returned status 2 /bin/tar: Error is not recoverable: exiting now tar (child): gzip: Cannot exec: No such file or directory tar (child): Error is not recoverable: exiting now /bin/tar: Child returned status 2 /bin/tar: Error is not recoverable: exiting now Error: Failed to install 'gbfetch' from GitHub: length(file_list) > 0 is not TRUE In addition: Warning messages: 1: In utils::untar(tarfile, ...) : ‘/bin/tar -xf '/local/tmp/RtmpTMKVqL/file84f26625fe8.tar.gz' -C '/local/tmp/RtmpTMKVqL/remotes84f1041a219'’ returned error code 2 2: In system(cmd, intern = TRUE) : running command '/bin/tar -tf '/local/tmp/RtmpTMKVqL/file84f26625fe8.tar.gz'' had status 2
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[joelnitta]

Thanks @grimmem1 for filing the issue.

TBH I haven't updated the package because I haven't been using it. Can you let me know a bit about your use case? I might be able to either suggest another approach or revive gbfetch.

[grimmem1]

I want a process to grab protein fasta files for alignment using msa. UniprotR and Rcpi have failed to retrieve anything directly running their usqge example. Thanks

[joelnitta]

Actually remotes::install_github("joelnitta/gbfetch") works on my machine, but anyways, this package is currently only designed for downloading DNA sequences, not amino acids.

May I suggest something like this?

library(rentrez)
katipo <- "Latrodectus katipo[Organism]"
katipo_search <- entrez_search(db="protein", term=katipo)
kaitpo_seqs <- entrez_fetch(db="protein", id=katipo_search$ids, rettype="fasta")