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### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('CNEr_1.49.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing CNEr ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── CNEr session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr
→ BiocVersion: 3.24
→ Package: CNEr
→ PackageVersion: 1.49.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/CNEr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr
→ installDir: /tmp/RtmpW8gdj2/file1aaf5743ddf1fd
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CNEr ───────────────────────────────────────────────────
* 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 3.5.0 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/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/AssemblyStats.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/blatCNE.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/ceScan-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/CNE-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/CNEDensity.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/cneMerge.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/fixCoordinates.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/grangesPairsForDotplot.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/makeAncoraFiles.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/makeCNEDensity.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/matchDistribution.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/plotCNEDistribution.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/plotCNEWidth.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/psubAxt.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/read.rmskFasta.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/readAncora.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/readAncoraIntoSQLite.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/readCNERangesFromSQLite.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/subAxt-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpW8gdj2/file1aaf5719f35e4d/CNEr/man/syntenicDotplot.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneSetEnrichment, GO
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (54%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of CNEr...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ceScan.R (line 6, column 25)
    • ...
    • R/IO-methods.R (line 161, column 45)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Ancora.R (line 12, column 25)
    • ...
    • KEGG.R (line 42, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Axt-class.R (line 111, column 3)
    • ...
    • cat() in R/Axt-class.R (line 186, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Axt-class.R (line 138, column 25)
    • ...
    • R/makeGeneDbFromUCSC.R (line 17, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/IO-methods.R (line 60, column 27)
    • R/IO-methods.R (line 109, column 27)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Axt-class.R (line 27, column 46)
    • ...
    • utils.R (line 193, column 22)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/utils.R (line 56, column 10)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/Ancora.R (line 151, column 19)
  • ...
  • suppressWarnings() in R/plot.R (line 52, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • lastz() (R/WholeGenomeAlignment.R): 151 lines
    • ...
    • ceScanR() (R/ceScan.R): 102 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/axisTrack.Rd
    • ...
    • man/grangesPairsForDotplot.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Axt-class.Rd
    • ...
    • man/writeAxt.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • axtChain.Rd
    • ...
    • netToAxt.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 27% of man
pages use at least one of these tags.
  Found in files:
    • addAncestorGO.Rd
    • ...
    • orgKEGGIds2EntrezIDs.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addAncestorGO.Rd
    • ...
    • orgKEGGIds2EntrezIDs.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; 105 lines (1%) are > 80 characters long.
  First few lines:
    • R/Axt-class.R#L224 newStart[indexNegative] <- querySeqlen ...
    • ...
    • vignettes/PairwiseWholeGenomeAlignment.Rmd#L164 As the last step, we
    create the _.net.ax ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • man/Axt-class.Rd#L76 } ...
    • ...
    • vignettes/CNEr.Rmd#L367 overwrite=TRUE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3426 lines (46%) are
not.
  First few lines:
    • R/Ancora.R#L5 ### diverging colour scheme from http: ...
    • ...
    • vignettes/PairwiseWholeGenomeAlignment.Rmd#L176
    binaryNetToAxt="netToAxt", ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the CNEr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.