[ Started: 2024-09-02 23:34:08 CEST ] [ MetaProViz v2.0.2 for BioC-3.20 from https://github.com/saezlab/MetaProViz@development (8f914ad 2024-08-22 13:28:56) ] Loading required package: BiocCheck ── Installing MetaProViz ─────────────────────────────────────────────────────── ✖ E: /tmp/RtmpPe6ax0/file3a9e201a7152ed/MetaProViz must be installable. ✖ E: /tmp/RtmpPe6ax0/file3a9e201a7152ed/MetaProViz must be loadable. ✔ Package installed successfully ── MetaProViz session metadata ───────────────────────────────────────────────── → sourceDir: /tmp/RtmpPe6ax0/file3a9e201a7152ed/MetaProViz → BiocVersion: 3.20 → Package: MetaProViz → PackageVersion: 2.0.2 → BiocCheckDir: /mnt/disk0/build/bioc-check/metaproviz/bioc-3.20/2024-09-02_2333/MetaProViz/MetaProViz.BiocCheck → BiocCheckVersion: 1.41.16 → sourceDir: /tmp/RtmpPe6ax0/file3a9e201a7152ed/MetaProViz → installDir: /tmp/RtmpPe6ax0/file3a9e20792c69d3 → isTarBall: TRUE → platform: unix ── Running BiocCheck on MetaProViz ───────────────────────────────────────────── * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... ! W: y of x.y.z version should be odd in devel * Checking R version dependency... * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... ✖ E: No biocViews terms found. ℹ Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... ℹ N: Provide 'URL', 'BugReports' field(s) in DESCRIPTION * Checking for Bioconductor software dependencies... ! W: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... ✖ E: 'VignetteEngine' specified but not in the DESCRIPTION. Add 'VignetteEngine' to DESCRIPTION from the following: • vignettes/CoRe Metabolomics.Rmd • ... • vignettes/Standard Metabolomics.Rmd ! W: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: • knitr ! W: Avoid T/F variables; If logical, use TRUE/FALSE Found in files: • vignettes/CoRe Metabolomics.Rmd (code line 31, column 42) • ... • vignettes/Standard Metabolomics.Rmd (code line 499, column 42) * Checking package installation calls in R code... ℹ N: Avoid using install, biocLite, install.packages, or update.packages Functions in files: • install.packages() in R/DifferentialMetaboliteAnalysis.R (line 68, column 5) • ... • install() in R/VizVolcano.R (line 89, column 18) Warning in tools::parse_Rd(manpage, macros = rdmacros) : /tmp/RtmpPe6ax0/file3a9e201a7152ed/MetaProViz/man/VizSuperplot.Rd:60: unexpected TEXT '(Default = NULL)', expecting '{' * Checking for library/require of MetaProViz... ! W: Avoid the use of 'library' or 'require' in R code Found in files: • library() in R/DifferentialMetaboliteAnalysis.R (line 77, column 20) • ... • require() in R/VizVolcano.R (line 86, column 10) * Checking coding practice... ℹ N: Avoid sapply(); use vapply() Found in files: • R/DifferentialMetaboliteAnalysis.R (line 1608, column 10) • ... • R/VizSuperplots.R (line 494, column 23) ℹ N: Avoid 1:...; use seq_len() or seq_along() Found in files: • DifferentialMetaboliteAnalysis.R (line 602, column 17) • ... • VizVolcano.R (line 1094, column 20) ℹ N: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • print() in R/GetPriorKnoweldge.R (line 340, column 11) • ... • print() in R/GetPriorKnoweldge.R (line 374, column 11) ℹ N: Avoid using '=' for assignment and use '<-' instead Found in files: • R/DifferentialMetaboliteAnalysis.R (line 263, column 25) • ... • R/VizSuperplots.R (line 133, column 26) ℹ N: Avoid the use of 'paste' in condition signals Found in files: • R/DifferentialMetaboliteAnalysis.R (line 208, column 124) • ... • R/VizSuperplots.R (line 106, column 62) ℹ N: Avoid redundant 'stop' and 'warn*' in signal conditions Found in files: • R/DifferentialMetaboliteAnalysis.R (line 138, column 15) • R/DifferentialMetaboliteAnalysis.R (line 158, column 19) • R/GetPriorKnoweldge.R (line 83, column 23) ! W: Avoid T/F variables; If logical, use TRUE/FALSE Found 14 times: • F in R/DifferentialMetaboliteAnalysis.R (line 856, column 86) • ... • T in R/VizPCA.R (line 215, column 25) ! W: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes Found in files: • Helper.R (line 260, column 23) • ... • OverRepresentationAnalysis.R (line 346, column 23) ! W: Remove set.seed usage (found 4 times) • set.seed() in R/VizHeatmap.R (line 188, column 9) • ... • set.seed() in R/VizHeatmap.R (line 600, column 5) * Checking parsed R code in R directory, examples, vignettes... ✖ E: Remove install() calls (found 30 times) • install.packages() in R/DifferentialMetaboliteAnalysis.R (line 68, column 5) • ... • install() in R/VizVolcano.R (line 89, column 18) ℹ N: Avoid 'suppressWarnings'/'*Messages' if possible (found 74 times) • suppressWarnings() in R/DifferentialMetaboliteAnalysis.R (line 131, column 23) • ... • suppressMessages() in R/VizVolcano.R (line 1169, column 7) * Checking function lengths... ℹ N: The recommended function length is 50 lines or less. There are 40 functions greater than 50 lines. The longest 5 functions are: • VizHeatmap() (R/VizHeatmap.R): 608 lines • ... • VizVolcano_Compare() (R/VizVolcano.R): 324 lines * Checking man page documentation... Warning in tools::parse_Rd(manpage, macros = rdmacros) : /tmp/RtmpPe6ax0/file3a9e201a7152ed/MetaProViz/man/VizSuperplot.Rd:60: unexpected TEXT '(Default = NULL)', expecting '{' ! W: Empty or missing \value sections found in man page(s). Found in files: • man/DMA.Rd • ... • man/VizVolcano.Rd Error in loadNamespace(pkgname, lib.loc = lib.loc) : there is no package called ‘MetaProViz’ Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted [ Finished: 2024-09-02 23:34:31 CEST ]