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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ssviz_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ssviz ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ssviz session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAoDBxl/file147715532c71ee/ssviz
→ BiocVersion: 3.24
→ Package: ssviz
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ssviz.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAoDBxl/file147715532c71ee/ssviz
→ installDir: /tmp/RtmpAoDBxl/file147715542f5211
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ssviz ──────────────────────────────────────────────────
* 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/RtmpAoDBxl/file147715532c71ee/ssviz/man/counts.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/ctrlbam.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/getCountMatrix-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/logicalORmissing-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/ntfreq-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/pctrlbam.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/pingpong-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/pingpong.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/plotDistro-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/plotFreq-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/plotPP-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/plotRegion-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/ptreatbam.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/readBam-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/ssviz-package.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/man/treatbam.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpAoDBxl/file147715532c71ee/ssviz/vignettes/ssviz.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage,
Alignment, SequenceMatching, QualityControl, DataImport
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 (29%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • ssviz.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ssviz.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ssviz...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllGenerics.R (line 92, column 53)
    • R/AllGenerics.R (line 93, column 53)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllGenerics.R (line 104, column 32)
    • ...
    • AllGenerics.R (line 348, column 24)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllGenerics.R (line 134, column 21)
    • ...
    • R/AllGenerics.R (line 345, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllGenerics.R (line 143, column 23)
    • ...
    • R/AllGenerics.R (line 356, column 23)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/AllGenerics.R (line 138, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/AllGenerics.R): 76 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/counts.Rd
    • ...
    • man/treatbam.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/getCountMatrix-methods.Rd
    • ...
    • man/readBam-methods.Rd
* Checking package NEWS...
* 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; 63 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L17 #reads bam files together wi ...
    • ...
    • vignettes/ssviz.Rnw#L165 \bibitem{Kawaoka2011} Shinpei Kawaoka, Y ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 167 lines (28%) are
not.
  First few lines:
    • R/AllGenerics.R#L11 function(file_name,tags=chara ...
    • ...
    • ssviz/NAMESPACE#L23 ) ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the ssviz.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.