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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('msImpute_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing msImpute ─────────────────────────────────────────────────────────
✔ Package installed successfully
── msImpute session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpoSCE2B/filee2f474576060e/msImpute
→ BiocVersion: 3.24
→ Package: msImpute
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/msImpute.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpoSCE2B/filee2f474576060e/msImpute
→ installDir: /tmp/RtmpoSCE2B/filee2f476d0d0321
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on msImpute ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG,
Clustering
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...
* 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 (14%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • msImpute-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of msImpute...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • mspip.R (line 188, column 32)
    • mspip.R (line 218, column 54)
    • mspip.R (line 376, column 58)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/computeStructuralMetrics.R (line 116, column 3)
    • cat() in R/scaleData.R (line 55, column 3)
    • cat() in R/scaleData.R (line 58, column 3)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/msImpute.R (line 88, column 13)
    • ...
    • R/mspip.R (line 528, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/mspip.R (line 495, column 15)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/msImpute.R (line 180, column 3)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • mspip() (R/mspip.R): 522 lines
    • evidenceToMatrix() (R/evidenceToMatrix.R): 59 lines
    • selectFeatures() (R/selectFeatures.R): 54 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/mspip.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • evidenceToMatrix.Rd
  • mspip.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; 346 lines (18%) are > 80 characters long.
  First few lines:
    • R/computeStructuralMetrics.R#L3 #' For an imputed dataset, it computes w
    ...
    • ...
    • vignettes/msImpute-vignette.Rmd#L433 Muench, D.E., Olsson, A., Ferchen,
    K. et ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 421 lines (22%) are
not.
  First few lines:
    • R/computeStructuralMetrics.R#L57 if(!is.null(group)){ ...
    • ...
    • vignettes/msImpute-vignette.Rmd#L387 ) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the msImpute.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.