SQMtools
Analyze Results Generated by the 'SqueezeMeta' Pipeline
Description
'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | OK |
Check details (15 non-OK)
CRAN incoming feasibility
Maintainer: ‘Fernando Puente-Sánchez <fernando.puente.sanchez@slu.se>’
Found the following (possibly) invalid URLs:
URL: http://eggnogdb.embl.de/#/app/results?seqid=P0A7G6&target_nogs=COG0468#COG0468_datamenu
From: man/RecA.Rd
Message: Invalid URL: '#' not allowed in fragment
package dependencies
Packages required but not available: 'pathview', 'Biostrings' Package suggested but not available for checking: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
CRAN incoming feasibility
Maintainer: ‘Fernando Puente-Sánchez <fernando.puente.sanchez@slu.se>’
Found the following (possibly) invalid URLs:
URL: http://eggnogdb.embl.de/#/app/results?seqid=P0A7G6&target_nogs=COG0468#COG0468_datamenu
From: man/RecA.Rd
Message: Invalid URL: '#' not allowed in fragment
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package dependencies
Package required but not available: ‘pathview’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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Check History
ERROR 11 OK · 1 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 9, 2026
CRAN incoming feasibility
Maintainer: ‘Fernando Puente-Sánchez <fernando.puente.sanchez@slu.se>’
Found the following (possibly) invalid URLs:
URL: http://eggnogdb.embl.de/#/app/results?seqid=P0A7G6&target_nogs=COG0468#COG0468_datamenu
From: man/RecA.Rd
Message: Invalid URL: '#' not allowed in fragment
CRAN incoming feasibility
Maintainer: ‘Fernando Puente-Sánchez <fernando.puente.sanchez@slu.se>’
Found the following (possibly) invalid URLs:
URL: http://eggnogdb.embl.de/#/app/results?seqid=P0A7G6&target_nogs=COG0468#COG0468_datamenu
From: man/RecA.Rd
Message: Invalid URL: '#' not allowed in fragment
package dependencies
Package required but not available: ‘pathview’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.