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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('puma_3.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing puma ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── puma session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpHJGtew/file1042c85341e061/puma
→ BiocVersion: 3.24
→ Package: puma
→ PackageVersion: 3.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/puma.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpHJGtew/file1042c85341e061/puma
→ installDir: /tmp/RtmpHJGtew/file1042c83f37be1d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on puma ───────────────────────────────────────────────────
* 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 3.2.0 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...
! WARNING: Invalid BiocViews term(s):
  • 'HTA2.0'
* Checking for recommended biocViews...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpHJGtew/file1042c85341e061/puma/man/calculateTtest.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpHJGtew/file1042c85341e061/puma/man/erfc.Rd'
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: 'Date:' field format is not 'YYYY-MM-DD': 2015-7-29
ℹ NOTE: Provide '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:
    • puma.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 40 out of 70 code chunks = 57% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • puma.Rnw
* Checking package installation calls in R code...
* Checking for library/require of puma...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/calculateLimma.R (line 7, column 9)
    • ...
    • require() in R/pumaPlots.R (line 151, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/orig_pplr.R (line 35, column 6)
    • ...
    • R/pumaComb.R (line 810, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calculateLimma.R (line 30, column 14)
    • ...
    • zzz.R (line 24, column 13)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • gmhta.R (line 130, column 61)
    • gmoExon.R (line 183, column 61)
    • igmoExon.R (line 236, column 61)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/bcomb.R (line 14, column 5)
    • ...
    • cat() in R/zzz.R (line 24, column 27)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/gmhta.R (line 39, column 20)
    • ...
    • R/pumaPlots.R (line 129, column 32)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • mgmos.R (line 11, column 21)
    • ...
    • pumaClust.R (line 6, column 49)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/pumaComb.R (line 56, column 50)
    • system() in R/pumaCombImproved.R (line 28, column 50)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/bcomb.R (line 33, column 3)
  • set.seed() in R/hcomb.R (line 19, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/pumaComb.R (line 147, column 43)
  • <<- in R/pumaCombImproved.R (line 118, column 43)
  • <<- in R/pumaPCA.R (line 337, column 24)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 25
functions greater than 50 lines.
  The longest 5 functions are:
    • igmoExon() (R/igmoExon.R): 721 lines
    • ...
    • pumaPCA() (R/pumaPCA.R): 364 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/clusterApplyLBDots.Rd
    • man/plot-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • bcomb.Rd
    • ...
    • pumaFull.Rd
* 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; 908 lines (8%) are > 80 characters long.
  First few lines:
    • R/calculateLimma.R#L60 plus_arrays <- as.matrix(which(design. ...
    • ...
    • vignettes/puma.Rnw#L850 There are examples of the automated crea ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3569 lines (32%) contain tabs.
  First few lines:
    • R/calculateLimma.R#L2 eset ...
    • ...
    • vignettes/puma.Rnw#L701 , row.names=rownames(pData(affybatch.exa ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2635 lines (23%) are
not.
  First few lines:
    • R/bcomb.R#L2 gsnorm=FALSE, nsample=1 ...
    • ...
    • vignettes/puma.Rnw#L616 r<-c(r,i) ...
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 | ⚠ 7 WARNINGS | ℹ 18 NOTES
ℹ See the puma.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.