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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('gcrma_2.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing gcrma ────────────────────────────────────────────────────────────
✔ Package installed successfully
── gcrma session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzytMWE/file1affc230c23d34/gcrma
→ BiocVersion: 3.24
→ Package: gcrma
→ PackageVersion: 2.85.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/gcrma.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpzytMWE/file1affc230c23d34/gcrma
→ installDir: /tmp/RtmpzytMWE/file1affc271738662
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gcrma ──────────────────────────────────────────────────
* 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 2.6.0 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...
* 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:
    • gcrma2.0.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 3 out of 3 code chunks = 100% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/gcrma2.0.Rnw
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/getPackages.R (line 31, column 9)
    • install.packages() in R/getPackages.R (line 80, column 9)
* Checking for library/require of gcrma...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/justGCRMA.R (line 89, column 46)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getPackages.R (line 22, column 25)
    • R/getPackages.R (line 71, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • base.profiles2.R (line 71, column 11)
    • ...
    • justGCRMA.R (line 270, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/base.profiles2.R (line 53, column 5)
    • ...
    • cat() in R/justGCRMA.R (line 303, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/base.profiles2.R (line 21, column 7)
    • ...
    • R/gcrma.R (line 59, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getPackages.R (line 14, column 47)
    • ...
    • R/getPackages.R (line 96, column 43)
! WARNING: Remove set.seed usage (found 4 times)
  • set.seed() in R/gcrma.engine.R (line 19, column 5)
  • ...
  • set.seed() in R/justGCRMA.R (line 261, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/bg.parameters.ns.R (line 11, column 3)
  • suppressWarnings() in R/bg.parameters.ns.R (line 64, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • just.gcrma() (R/justGCRMA.R): 121 lines
    • ...
    • compute.affinities() (R/compute.affinities.R): 68 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/affinity.spline.coefs.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • bg.adjust.affinities.Rd
    • ...
    • justGCRMA.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; 121 lines (5%) are > 80 characters long.
  First few lines:
    • R/base.profiles2.R#L53 cat("\nNote: some of your negative c ...
    • ...
    • vignettes/gcrma2.0.Rnw#L277 sequence. The user can turn off this fea ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1015 lines (45%) are
not.
  First few lines:
    • R/base.profiles2.R#L2 if (is.numeric(stop) && length(stop) = ...
    • ...
    • vignettes/gcrma2.0.Rnw#L284 \end{enumerate} ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 15 NOTES
ℹ See the gcrma.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.