############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('SparseArray_1.12.2.tar.gz','quit-with-status'=TRUE)" ### ############################################################################## ############################################################################## ── Installing SparseArray ────────────────────────────────────────────────────── ✔ Package installed successfully ── SparseArray session metadata ──────────────────────────────────────────────── → sourceDir: /tmp/Rtmp1SOpGz/file174e0161ad1908/SparseArray → BiocVersion: 3.23 → Package: SparseArray → PackageVersion: 1.12.2 → BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/SparseArray.BiocCheck → BiocCheckVersion: 1.48.0 → sourceDir: /tmp/Rtmp1SOpGz/file174e0161ad1908/SparseArray → installDir: /tmp/Rtmp1SOpGz/file174e011fb9a8bd → isTarBall: TRUE → platform: unix ── Running BiocCheck on SparseArray ──────────────────────────────────────────── * 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 4.3.0 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: ATACSeq, RNASeq 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 (55%). * Checking for pinned package versions in DESCRIPTION... * Checking for 'fnd' role in Authors@R... * 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: • SparseArray_objects.Rmd * Checking package installation calls in R code... * Checking for library/require of SparseArray... ! WARNING: Avoid the use of 'library' or 'require' in R code Found in files: • library() in R/thread-control.R (line 117, column 5) • library() in R/thread-control.R (line 122, column 5) * Checking coding practice... ℹ NOTE: Avoid sapply(); use vapply() Found in files: • R/SparseArray-matrixStats.R (line 162, column 16) ℹ NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: • SparseArray-matrixStats.R (line 184, column 42) • thread-control.R (line 124, column 14) ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • cat() in R/readSparseCSV.R (line 19, column 5) • cat() in R/readSparseCSV.R (line 78, column 9) • cat() in R/readSparseCSV.R (line 89, column 9) ! WARNING: .Deprecated / .Defunct usage (found 1 times) • .Deprecated() in R/readSparseCSV.R (line 236, column 5) * Checking parsed R code in R directory, examples, vignettes... ℹ Found @ in man/SVT_SparseArray-class.Rd ℹ NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) • suppressWarnings() in R/readSparseCSV.R (line 114, column 23) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 7 functions greater than 50 lines. The longest 5 functions are: • .OLD_rowStats_SparseArray() (R/SparseArray-matrixStats.R): 69 lines • ... • .rowStats_NaArray() (R/NaArray-matrixStats.R): 52 lines * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/NaArray-abind.Rd • ... • man/SparseArray-subsetting.Rd ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • NaArray-aperm.Rd • read_block_as_sparse.Rd • SparseArray-aperm.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; 22 lines (0%) are > 80 characters long. First few lines: • man/NaArray-matrixStats.Rd#L66 \S4method{colAnys}{NaArray}(x, rows=NULL ... • ... • man/SparseArray-matrixStats.Rd#L122 \S4method{colMedians}{SparseArray}(x, ro ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 1265 lines (10%) are not. First few lines: • R/COO_SparseArray-class.R#L25 # nonzero eleme ... • ... • vignettes/SparseArray_objects.Rmd#L441 SVT\_SparseArray objects. ... 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 | ⚠ 3 WARNINGS | ℹ 13 NOTES ℹ See the SparseArray.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.