##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('safe_3.53.1.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing safe ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── safe session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmppRojte/file127f2955c1d96c/safe
→ BiocVersion: 3.24
→ Package: safe
→ PackageVersion: 3.53.1
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/safe.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmppRojte/file127f2955c1d96c/safe
→ installDir: /tmp/RtmppRojte/file127f29648032cb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on safe ───────────────────────────────────────────────────
* 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 2.4.0 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/RtmppRojte/file127f2955c1d96c/safe/man/gene.results.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppRojte/file127f2955c1d96c/safe/man/p53.stat.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppRojte/file127f2955c1d96c/safe/man/safe-internal.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppRojte/file127f2955c1d96c/safe/man/safe.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppRojte/file127f2955c1d96c/safe/man/safedag.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppRojte/file127f2955c1d96c/safe/man/safeplot.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Sequencing, Microarray
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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • SAFEmanual3.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • SAFEmanual3.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/SAFEmanual3.Rnw (chunk no. 25, line 220, column 47)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/SAFEmanual3.Rnw
* Checking package installation calls in R code...
* Checking for library/require of safe...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/getCmatrix.R (line 69, column 7)
    • ...
    • require() in R/safeplot.R (line 33, column 12)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getCmatrix.R (line 50, column 15)
    • ...
    • R/safeplot.R (line 114, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • error.FDR.BH.R (line 5, column 56)
    • ...
    • safeplot.R (line 115, column 17)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • getCmatrix.R (line 100, column 53)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/getCmatrix.R (line 32, column 7)
    • ...
    • cat() in R/safeplot.R (line 15, column 10)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/SAFE-class.R (line 57, column 9)
    • ...
    • R/safedag.R (line 16, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/safe.R (line 60, column 14)
    • ...
    • R/safe.R (line 363, column 15)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/safe.R (line 278, column 25)
    • R/safe.R (line 297, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • F in R/safe.R (line 161, column 52)
    • ...
    • T in R/sigfig.R (line 5, column 41)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/SAFEmanual3.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* 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:
    • safe() (R/safe.R): 364 lines
    • ...
    • gene.results() (R/gene.results.R): 72 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gene.results.Rd
    • ...
    • man/safeplot.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • gene.results.Rd
    • ...
    • safedag.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; 279 lines (12%) are > 80 characters long.
  First few lines:
    • R/gene.results.R#L7 cat(paste("WARNING: error = \"", ...
    • ...
    • vignettes/SAFEmanual3.Rnw#L497 \item Zhou, Y.H., Barry, W.T., and Wrigh
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/SAFE-class.R#L69 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 568 lines (25%) are
not.
  First few lines:
    • R/gene.results.R#L3 print.it = TRUE, gene.names = ...
    • ...
    • vignettes/SAFEmanual3.Rnw#L421 \includegraphics[width=3.5in]{SAFEmanu ...
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 ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 5 WARNINGS | ℹ 20 NOTES
ℹ See the safe.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.