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Proteomicslab57357 / UniprotR

Retrieving Information of Proteins from Uniprot
GNU General Public License v3.0
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there is no package called ‘Biostrings’ #34

Closed biochembryony closed 1 year ago

biochembryony commented 1 year ago

Hi,

Thank you for making this package available to use. I am excited to use it for my research, however I get the following issue when I try to use it.

Error: package or namespace load failed for ‘UniprotR’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Biostrings’

This message appears when I try to load UniprotR in an R notebook, using the command library(UniprotR). I have tried using the command install.packages("Biostrings"), but I get the message "Warning in install.packages : package ‘Biostrings’ is not available for this version of R". I have the latest version of R Studio (Beagle Scouts) - is this incompatible or am I doing something else wrong?

Hope you can offer some help, any advice would be greatly appreciated.

lkalmar commented 1 year ago

Had the same problem, just had to install Biostrings: BiocManager::install("Biostrings")

You will probably have one more error, missing the GenomicAlignments package, install the same way: BiocManager::install("GenomicAlignments")

If you don't have the BiocManager installed, you have to install it before these: install.packages("BiocManager")

MohmedSoudy commented 1 year ago

Hi @biochembryony, This problem is similar to #14 It's due to dependency "alakazam" version 1.1.0 while UniprotR requires alakazam version 1.0.0. This problem will be solved in the next version of UniprotR and can be solved now by installing alakazam before installing UniprotR using install.packages("https://cran.r-project.org/src/contrib/Archive/alakazam/alakazam_1.0.0.tar.gz", repo=NULL, type="source")