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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('systemPipeR_2.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing systemPipeR ──────────────────────────────────────────────────────
✔ Package installed successfully
── systemPipeR session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpfmp838/file149f431df27419/systemPipeR
→ BiocVersion: 3.24
→ Package: systemPipeR
→ PackageVersion: 2.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/systemPipeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpfmp838/file149f431df27419/systemPipeR
→ installDir: /tmp/Rtmpfmp838/file149f432b062361
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on systemPipeR ────────────────────────────────────────────
* 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 4.1.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/alignStats.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/clusterRun.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/countRangeset.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/olRanges.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/renderLogs.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/renderReport.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/runCommandline.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/subsetWF.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/symLink2bam.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/systemPipeR-package.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/tryCMD.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpfmp838/file149f431df27419/systemPipeR/man/tryPath.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
SequenceMatching
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 '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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • systemPipeR.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/systemPipeR_workflows.Rmd
* Checking package installation calls in R code...
* Checking for library/require of systemPipeR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/geneSetAnalysis.R (line 99, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/chipseq.R (line 93, column 16)
    • ...
    • R/varseq.R (line 110, column 31)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • fastqQuality.R (line 40, column 30)
    • ...
    • varseq.R (line 34, column 67)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/chipseq.R (line 62, column 13)
    • ...
    • print() in R/varseq.R (line 172, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/sysargslist_utilities.R (line 402, column 25)
    • R/sysargslist_utilities.R (line 402, column 42)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cmdToCWL_v2.R (line 178, column 46)
    • ...
    • R/sysargslist_utilities.R (line 2078, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 8 times:
    • F in R/chipseq.R (line 93, column 94)
    • ...
    • T in R/utilities.R (line 996, column 63)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • chipseq.R (line 278, column 25)
    • ...
    • utilities.R (line 854, column 24)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/developerFct.R (line 11, column 5)
    • ...
    • system() in R/utilities.R (line 1146, column 27)
✖ ERROR: Avoid references to external hosting platforms
  Found in files:
    • sysargslist_utilities.R (line 1849, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 5 times)
  • <<- in R/cmdToCWL_v2.R (line 209, column 12)
  • ...
  • <<- in R/utilities.R (line 1011, column 21)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 20 times)
  • suppressWarnings() in R/fastqQuality.R (line 213, column 13)
  • ...
  • suppressMessages() in R/utilities.R (line 1032, column 27)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 70
functions greater than 50 lines.
  The longest 5 functions are:
    • vennPlot() (R/overLapper.R): 323 lines
    • ...
    • SYSargsList() (R/sysargslist_utilities.R): 208 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/catmap.Rd
    • man/sysargs.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/add-methods.Rd
    • ...
    • man/trimbatch.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • catmap.Rd
  • ...
  • tryCMD.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 47% of man
pages use at least one of these tags.
  Found in files:
    • alignStats.Rd
    • ...
    • writeTargetsRef.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • alignStats.Rd
    • ...
    • writeTargetsRef.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-01-SYSargs.R
test-02-SYSargs2.R test-03-SYSargsList.R test-05-catDB.R test-06-VENNset.R
test-07-features.R test-08-cmd2cwl.R test-10-chipSeq.R test-utilities.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 3261 lines (14%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L7 setGeneric(name = "targetsheader", def = ...
    • ...
    • vignettes/systemPipeR.Rmd#L2875 and the National Institute on Aging of t
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 184 lines (1%) contain tabs.
  First few lines:
    • R/overLapper.R#L160 The input 'setlist' needs to be a ...
    • ...
    • man/VENNset-class.Rd#L45 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1396 lines (6%) are
not.
  First few lines:
    • R/chipseq.R#L8 out_dir = f ...
    • ...
    • vignettes/systemPipeR.Rmd#L2854 clu ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 23 NOTES
ℹ See the systemPipeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.