##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CoCiteStats_1.85.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing CoCiteStats ──────────────────────────────────────────────────────
✔ Package installed successfully
── CoCiteStats session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNbzYME/file777d93a6d00e4/CoCiteStats
→ BiocVersion: 3.24
→ Package: CoCiteStats
→ PackageVersion: 1.85.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CoCiteStats.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNbzYME/file777d93a6d00e4/CoCiteStats
→ installDir: /tmp/RtmpNbzYME/file777d916c1628
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CoCiteStats ────────────────────────────────────────────
* 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 2.0 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...
✖ ERROR: Add biocViews other than Software
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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of CoCiteStats...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/gene.geneslist.sig.R (line 9, column 27)
    • R/gene.geneslist.sig.R (line 22, column 41)
    • R/gene.geneslist.statistic.R (line 7, column 19)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • gene.geneslist.sig.R (line 15, column 14)
    • twTStats.R (line 20, column 41)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/actorAdjTable.R (line 4, column 9)
    • ...
    • R/twTStats.R (line 13, column 7)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long.
  First few lines:
    • CoCiteStats/NAMESPACE#L3 export(actorAdjTable, gene.geneslist.sig ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/paperLen.R#L10 paperCts = paperCts[unique(unlist(paper ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 172 lines (37%) are
not.
  First few lines:
    • R/gene.gene.statistic.R#L4 ## no adjustment ...
    • ...
    • man/twTStats.Rd#L38 twTStats(tw1) ...
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 email is ok.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 0 WARNINGS | ℹ 12 NOTES
ℹ See the CoCiteStats.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.