############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('DelayedArray_0.38.1.tar.gz','quit-with-status'=TRUE)" ### ############################################################################## ############################################################################## ── Installing DelayedArray ───────────────────────────────────────────────────── ✔ Package installed successfully ── DelayedArray session metadata ─────────────────────────────────────────────── → sourceDir: /tmp/RtmpLbNHup/file1562996e6c1291/DelayedArray → BiocVersion: 3.23 → Package: DelayedArray → PackageVersion: 0.38.1 → BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/DelayedArray.BiocCheck → BiocCheckVersion: 1.48.0 → sourceDir: /tmp/RtmpLbNHup/file1562996e6c1291/DelayedArray → installDir: /tmp/RtmpLbNHup/file1562994773c22 → isTarBall: TRUE → platform: unix ── Running BiocCheck on DelayedArray ─────────────────────────────────────────── * 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... ℹ Package version 0.38.1; pre-release * Checking R version dependency... ℹ NOTE: Update R version dependency from 4.0.0 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... ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG 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... * Checking for Bioconductor software dependencies... ℹ Bioconductor dependencies found in Imports & Depends (60%). * 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... ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • A-Working_with_large_arrays.Rnw • C-DelayedArray_HDF5Array_update.Rnw ℹ NOTE: Vignette(s) found with missing chunk labels Found in files: • A-Working_with_large_arrays.Rnw ℹ NOTE: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/A-Working_with_large_arrays.Rnw • vignettes/C-DelayedArray_HDF5Array_update.Rnw * Checking package installation calls in R code... * Checking for library/require of DelayedArray... * Checking coding practice... ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • cat() in R/showtree.R (line 54, column 9) ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions Found in files: • R/AutoGrid.R (line 201, column 23) ! WARNING: .Deprecated / .Defunct usage (found 1 times) • .Deprecated() in R/RealizationSink-class.R (line 117, column 5) * Checking parsed R code in R directory, examples, vignettes... ℹ Found @ in man/DelayedAbind-class.Rd ℹ Found @ in man/DelayedAperm-class.Rd ℹ Found @ in man/DelayedNaryIsoOp-class.Rd ℹ Found @ in man/DelayedSetDimnames-class.Rd ℹ Found @ in man/DelayedSubassign-class.Rd ℹ Found @ in man/DelayedSubset-class.Rd ℹ Found @ in man/DelayedUnaryIsoOpStack-class.Rd ℹ Found @ in man/DelayedUnaryIsoOpWithArgs-class.Rd ℹ Found @ in man/simplify.Rd ℹ NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times) • suppressWarnings() in R/DelayedArray-utils.R (line 607, column 30) • suppressWarnings() in R/DelayedArray-utils.R (line 672, column 30) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 14 functions greater than 50 lines. The longest 5 functions are: • BLOCK_rowsum() (R/DelayedMatrix-rowsum.R): 98 lines • ... • .compute_rowVars_for_horizontal_strips() (R/matrixStats-methods.R): 72 lines * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/DelayedAbind-class.Rd • ... • man/matrixStats-methods.Rd Warning: .onUnload failed in unloadNamespace() for 'DelayedArray', details: call: library.dynam.unload("DelayedArray", libpath) error: shared object ‘DelayedArray.so’ was not loaded ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • chunkGrid.Rd • compat.Rd • DelayedOp-class.Rd ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man pages use at least one of these tags. Found in files: • DelayedArray-class.Rd • DelayedArray-utils.Rd • RleArray-class.Rd ℹ NOTE: Use donttest instead of dontrun. Found in files: • DelayedArray-class.Rd • DelayedArray-utils.Rd • RleArray-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; 17 lines (0%) are > 80 characters long. First few lines: • R/DelayedMatrix-mult.R#L550 # this, and all other calls, had bet ... • ... • vignettes/C-DelayedArray_HDF5Array_update.Rnw#L11 % https://tex.stackexchange.com/questi ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 2068 lines (12%) are not. First few lines: • R/AutoBlock-global-settings.R#L34 "auto.block.size shoul ... • ... • vignettes/C-DelayedArray_HDF5Array_update.Rnw#L210 \end{block} ... 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. ✖ ERROR: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile ── BiocCheck v1.48.0 results ─────────────────────────────────────────────────── ✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES ℹ See the DelayedArray.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.