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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('canceR_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing canceR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── canceR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAgiZi7/file61335666eabd6/canceR
→ BiocVersion: 3.24
→ Package: canceR
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/canceR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAgiZi7/file61335666eabd6/canceR
→ installDir: /tmp/RtmpAgiZi7/file613356f12b043
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on canceR ─────────────────────────────────────────────────
* 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 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.Analyze.Sets.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.ConsPlot.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.EnrichmentScore.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.EnrichmentScore2.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.Gct2Frame.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.Gct2Frame2.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.GeneRanking.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.HeatMapPlot.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.HeatMapPlot2.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.NormalizeCols.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.NormalizeRows.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.ReadClsFile.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.Res2Frame.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.Threshold.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.VarFilter.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/GSEA.write.gct.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/myGlobalEnv.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAgiZi7/file61335666eabd6/canceR/man/OLD.GSEA.EnrichmentScore.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
ThirdPartyClient
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (19%).
* 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: Evaluate more vignette chunks.
ℹ 5 out of 6 code chunks = 83% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/canceR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of canceR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/cgdsr.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cbind.na.R (line 57, column 15)
    • ...
    • R/rbind.na.R (line 81, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dialoggetGeneListMSigDB.R (line 42, column 16)
    • ...
    • rbind.na.R (line 97, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cgdsr.R (line 43, column 5)
    • ...
    • print() in R/Match_GeneList_MSigDB.R (line 71, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cgdsr.R (line 37, column 13)
    • ...
    • R/testCheckedCaseGenProf.R (line 44, column 25)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/dialogSummary_GSEA.R (line 49, column 18)
    • R/dialogSummary_GSEA.R (line 78, column 18)
    • R/getGCT_CLSfiles.R (line 119, column 30)
! WARNING: Remove set.seed usage (found 4 times)
  • set.seed() in R/getGCT_CLSfiles.R (line 125, column 21)
  • ...
  • set.seed() in R/GSEA.1.0.R (line 949, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 5 times)
  • <<- in R/geteSet.R (line 75, column 30)
  • ...
  • <<- in R/getGCT_CLSfiles.R (line 164, column 34)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 60
functions greater than 50 lines.
  The longest 5 functions are:
    • GSEA() (R/GSEA.1.0.R): 1297 lines
    • ...
    • getCasesGenProfs() (R/getCasesGenProfs.R): 301 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/GSEA.EnrichmentScore.Rd
  • ...
  • man/OLD.GSEA.EnrichmentScore.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/CGDS.Rd
    • man/test.CGDS.Rd
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
Warning: loading Rplot failed

ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • about.Rd
  • ...
  • test.CGDS.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 96% of man
pages use at least one of these tags.
  Found in files:
    • about.Rd
    • ...
    • UnifyRowNames.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • about.Rd
    • ...
    • UnifyRowNames.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; 1452 lines (12%) are > 80 characters long.
  First few lines:
    • R/aaa.R#L5 "ListMutData", "lenght ...
    • ...
    • vignettes/canceR.Rmd#L814 <!-- \item search nearest Cancer by ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/GSEA.1.0.R#L466 if (row.sd[i] == 0) { ...
    • ...
    • R/GSEA.1.0.R#L2152 return() ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1749 lines (15%) are
not.
  First few lines:
    • R/aaa.R#L3 "ttMain", "x", "fname. ...
    • ...
    • vignettes/canceR.Rmd#L810 ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the canceR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.