############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('BiocFileCache_3.2.0.tar.gz','quit-with-status'=TRUE)" ### ############################################################################## ############################################################################## ── Installing BiocFileCache ──────────────────────────────────────────────────── ✔ Package installed successfully ── BiocFileCache session metadata ────────────────────────────────────────────── → sourceDir: /tmp/RtmpZ2HCDp/file15305668a6b5e8/BiocFileCache → BiocVersion: 3.23 → Package: BiocFileCache → PackageVersion: 3.2.0 → BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocFileCache.BiocCheck → BiocCheckVersion: 1.48.0 → sourceDir: /tmp/RtmpZ2HCDp/file15305668a6b5e8/BiocFileCache → installDir: /tmp/RtmpZ2HCDp/file153056149b9cc4 → isTarBall: TRUE → platform: unix ── Running BiocCheck on BiocFileCache ────────────────────────────────────────── * 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... * Checking R version dependency... ℹ NOTE: Update R version dependency from 3.4.0 to 4.6.0 * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... → Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * 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... ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION * Checking for Bioconductor software dependencies... ! WARNING: 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 for 'fnd' role in Authors@R... ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant, consider adding the 'fnd' role to the list of authors. * Checking NAMESPACE... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... ℹ NOTE: Vignette(s) found with missing chunk labels Found in files: • BiocFileCache_Troubleshooting.Rmd • BiocFileCache_UseCases.Rmd • BiocFileCache.Rmd * Checking package installation calls in R code... * Checking for library/require of BiocFileCache... * Checking coding practice... ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • cat() in R/httr.R (line 177, column 9) • ... • cat() in R/makeCachedActiveBinding.R (line 40, column 17) ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/BiocFileCache-class.R (line 7, column 20) • ... • R/httr.R (line 153, column 21) ℹ NOTE: Avoid the use of 'paste' in condition signals Found in files: • R/BiocFileCache-class.R (line 1224, column 13) ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions Found in files: • R/BiocFileCache-class.R (line 563, column 55) • ... • R/utilities.R (line 198, column 14) * Checking parsed R code in R directory, examples, vignettes... ℹ NOTE: Avoid '<<-' if possible (found 3 times) • <<- in R/utilities.R (line 24, column 22) • <<- in R/utilities.R (line 28, column 22) • <<- in R/utilities.R (line 33, column 22) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 8 functions greater than 50 lines. The longest 5 functions are: • _anonymous_.68() (R/makeBiocFileCacheFromDataFrame.R): 145 lines • ... • _anonymous_.535() (R/BiocFileCache-class.R): 66 lines * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/makeCachedActiveBinding.Rd ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 50% of man pages use at least one of these tags. Found in files: • BFCOption.Rd • BiocFileCache-class.Rd ℹ NOTE: Use donttest instead of dontrun. Found in files: • BiocFileCache-class.Rd * Checking package NEWS... * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... ℹ NOTE: Consider shorter lines; 28 lines (1%) are > 80 characters long. First few lines: • R/BiocFileCache-class.R#L326 action=action, proxy=proxy, d ... • ... • vignettes/BiocFileCache.Rmd#L699 and file permissions, you may run the fo ... ℹ NOTE: Consider 4 spaces instead of tabs; 31 lines (1%) contain tabs. First few lines: • vignettes/BiocFileCache_Troubleshooting.Rmd#L169 moveFiles<-function(package){ ... • ... • vignettes/BiocFileCache.Rmd#L623 metadataName="resourceMetadata") ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 143 lines (3%) are not. First few lines: • R/BiocFileCache-class.R#L254 fname=c("unique", "exact")) ... • ... • vignettes/BiocFileCache.Rmd#L632 * `removebfc()` ... ℹ See https://contributions.bioconductor.org/r-code.html ℹ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... * Checking for bioc-devel mailing list subscription... ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... ℹ Maintainer is registered at support site. ℹ Package is in the Support Site Watched Tags. ── BiocCheck v1.48.0 results ─────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES ℹ See the BiocFileCache.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.