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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('metaSeq_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing metaSeq ──────────────────────────────────────────────────────────
✔ Package installed successfully
── metaSeq session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq
→ BiocVersion: 3.24
→ Package: metaSeq
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/metaSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq
→ installDir: /tmp/RtmpD4gaMC/filed4c987c2e3af3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on metaSeq ────────────────────────────────────────────────
* 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 2.13.0 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/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/BreastCancer.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/Fisher.test.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/meta.oneside.noiseq.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/meta.readData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/metaSeq-package.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/other.oneside.pvalues.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/pvals.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/Stouffer.test.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/StudyA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/text.busca_unix.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/text.busca_win.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/text.n.menor_unix.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/man/text.n.menor_win.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpD4gaMC/filed4c9813f1bdbf/metaSeq/vignettes/metaSeq.Rnw'
* 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': 2013-12-2
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • metaSeq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • metaSeq.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/metaSeq.Rnw (chunk no. 7, line 53, column 1)
    • ...
    • vignettes/metaSeq.Rnw (chunk no. 11, line 95, column 1)
* Checking package installation calls in R code...
* Checking for library/require of metaSeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/meta.oneside.noiseq.R (line 102, column 20)
    • R/other.oneside.pvalues.R (line 24, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • custom.MD.R (line 2, column 32)
    • ...
    • other.oneside.pvalues.R (line 37, column 35)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/meta.oneside.noiseq.R (line 26, column 12)
    • ...
    • R/oneside.noiseq.R (line 19, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/meta.oneside.noiseq.R (line 8, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/meta.oneside.noiseq.R (line 58, column 11)
  • <<- in R/meta.readData.R (line 37, column 11)
  • <<- in R/oneside.noiseq.R (line 47, column 8)
* 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:
    • meta.oneside.noiseq() (R/meta.oneside.noiseq.R): 125 lines
    • oneside.noiseq() (R/oneside.noiseq.R): 75 lines
    • meta.readData() (R/meta.readData.R): 57 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/BreastCancer.Rd
    • ...
    • man/text.n.menor_win.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Accelerate.NOISeq.Rd
    • ...
    • man/Stouffer.test.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • Accelerate.NOISeq.Rd
    • Reset.Accelerate.NOISeq.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; 101 lines (7%) are > 80 characters long.
  First few lines:
    • R/meta.oneside.noiseq.R#L8 stop("Error. You must give an ob ...
    • ...
    • vignettes/metaSeq.Rnw#L303 \newblock \emph {Transcript assembly and ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • metaSeq/NAMESPACE#L6 meta.readData, ...
    • ...
    • metaSeq/NAMESPACE#L12 Reset.Accelerate.NOISeq ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 59 lines (4%) are not.
  First few lines:
    • R/meta.oneside.noiseq.R#L84 k = e$k, norm = e$norm ...
    • ...
    • vignettes/metaSeq.Rnw#L279 ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the metaSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.