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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('msmsTests_1.51.0.tar.gz','quit-with-status'=TRUE)"
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── Installing msmsTests ────────────────────────────────────────────────────────
✔ Package installed successfully
── msmsTests session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvWS8tN/filee391870a8ac09/msmsTests
→ BiocVersion: 3.24
→ Package: msmsTests
→ PackageVersion: 1.51.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/msmsTests.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvWS8tN/filee391870a8ac09/msmsTests
→ installDir: /tmp/RtmpvWS8tN/filee39187e9d960c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on msmsTests ──────────────────────────────────────────────
* 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 3.0.1 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:
GeneExpression, DifferentialExpression, BatchEffect, Regression,
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 (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...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • msmsTests-Vignette.Rnw
    • msmsTests-Vignette2.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • msmsTests-Vignette.Rnw
    • msmsTests-Vignette2.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/msmsTests-Vignette.Rnw
    • vignettes/msmsTests-Vignette2.Rnw
* Checking package installation calls in R code...
* Checking for library/require of msmsTests...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • msmsTest-functions.R (line 38, column 12)
    • msmsTest-functions.R (line 75, column 12)
    • msmsTest-functions.R (line 180, column 12)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/msmsTest-functions.R (line 15, column 6)
    • R/msmsTest-functions.R (line 52, column 6)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/msmsTest-functions.R (line 125, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 40 lines (3%) are > 80 characters long.
  First few lines:
    • msmsTests/NAMESPACE#L1 export(msms.glm.pois, msms.glm.qlll, msm ...
    • ...
    • vignettes/msmsTests-Vignette2.Rnw#L302 false discovery rate: a practical
    and po ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • R/msmsTest-functions.R#L104 res <- glmLRT(fit,coef=vc) ...
    • vignettes/msmsTests-Vignette2.Rnw#L246 "blocking","blocki ...
    • vignettes/msmsTests-Vignette2.Rnw#L261 "blocking","blocki ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 264 lines (17%) are
not.
  First few lines:
    • R/msmsTest-functions.R#L16 data <- data.frame(y=round(count),facs ...
    • ...
    • vignettes/msmsTests-Vignette2.Rnw#L307 ...
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 | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the msmsTests.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.