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bdaisley / isolateR

Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries
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Error installing isolateR in R 4.4.0 on Windows 10 and 11 #7

Open vancurens opened 3 months ago

vancurens commented 3 months ago

When running the install command in a new R environment on Windows systems it has been noted that Bioconductor dependencies fail to install, resulting in a failed isolateR installation:

Installing package into ‘C:/Users/cambr/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
ERROR: dependencies 'Biostrings', 'msa', 'sangeranalyseR', 'sangerseqR' are not available for package 'isolateR'
* removing 'C:/Users/cambr/AppData/Local/R/win-library/4.4/isolateR'
Warning messages:
1: In i.p(...) :
  installation of package ‘sangerseqR’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In i.p(...) :
  installation of package ‘sangeranalyseR’ had non-zero exit status
4: In i.p(...) :
  installation of package ‘C:/Users/cambr/AppData/Local/Temp/RtmpUjesIT/file8dc715e6ae2/isolateR_0.0.0.9003.tar.gz’ had non-zero exit status

The current work around for this issue is to install the Bioconductor packages separately, as demonstrated below.

BiocManager::install("sangerseqR", force =TRUE)
BiocManager::install("GenomeInfoDb", force =TRUE)
BiocManager::install("sangeranalyseR", force =TRUE)
BiocManager::install("msa", force =TRUE)
devtools::install_github("bdaisley/isolateR")

IsolateR will then successfully install and can be called like normal with library(isolateR).