Comments (4)
Could you post your session info? You could also try installing from source:
#see here for more info https://forum.qiime2.org/t/problems-installing-qiime2r/11999/6
download.file("https://github.com/jbisanz/qiime2R/archive/master.zip", "source.zip")
unzip("source.zip")
install.packages("qiime2R-master", repos = NULL, type="source")
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Here is my session info
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.4.2
loaded via a namespace (and not attached):
[1] compiler_4.2.3 tools_4.2.3 rstudioapi_0.14 curl_5.0.1
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Just tried your previous suggestion
download.file("https://github.com/jbisanz/qiime2R/archive/master.zip", "source.zip")
unzip("source.zip")
install.packages("qiime2R-master", repos = NULL, type="source")
and received this error
ERROR: dependencies 'Biostrings', 'rhdf5', 'zCompositions', 'phyloseq' are not available for package 'qiime2R'
* removing 'C:/Users/bugsj/AppData/Local/R/win-library/4.2/qiime2R'
Warning in install.packages :
installation of package ‘qiime2R-master’ had non-zero exit status
Should I download the above dependencies and re-try?
from qiime2r.
Yes, when in doubt, manually install the dependencies. Not sure why you would have this problem, could be something about where they are being installed on windows.
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Related Issues (20)
- Error in read_yaml...could not find function "read_yaml"
- Feature request: support for importing q2-longitudinal artifacts HOT 3
- Newer version of dplyr no longer works with example HOT 1
- Exporting R objects to qza files
- qiime2 to Phyloseq HOT 1
- taxa_barplot plots all taxa as remainder when a sample has 0 reads
- close HOT 1
- summarize_taxa HOT 1
- Unable to Install qiime2R HOT 3
- taxa_barplot and taxa_heatmap ordering x-axis by alphabetical order HOT 1
- Problem installing qiime2R in R 4.3.1 HOT 1
- QZA to FASTA? HOT 1
- Phyloseq Object have 0 in OTU table HOT 2
- How to import nucleotide sequences [refseq() or DNAStringSet] using qiime2R
- taxa_heatmap() sample order
- Support for TreeSummarizedExperiment container? HOT 7
- OTU with sequence instead of unique identifier as row names? HOT 1
- `Error in file(con, 'r") : cannot open the connection` when user inputs incorrect filename into metadata parameter in `qza_to_phyloseq`` HOT 1
- Error when i call phyloseq object imported by qza_to_phyloseq
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