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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('graph_1.90.0.tar.gz','quit-with-status'=TRUE)"
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── Installing graph ────────────────────────────────────────────────────────────
✔ Package installed successfully
── graph session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpK5kI15/file7c9262dd6dfdb/graph
→ BiocVersion: 3.23
→ Package: graph
→ PackageVersion: 1.90.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/graph.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpK5kI15/file7c9262dd6dfdb/graph
→ installDir: /tmp/RtmpK5kI15/file7c9266221eb82
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on graph ──────────────────────────────────────────────────
* 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 2.10 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/RtmpK5kI15/file7c9262dd6dfdb/graph/man/toDotWithRI.Rd'
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 (20%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GraphClass.Rmd
    • MultiGraphClass.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/clusterGraph.Rmd
    • ...
    • vignettes/MultiGraphClass.Rmd
* Checking package installation calls in R code...
* Checking for library/require of graph...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/zzz.R (line 18, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bitarray.R (line 75, column 5)
    • ...
    • R/settings.R (line 218, column 46)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • methods-graphBAM.R (line 587, column 24)
    • MultiGraph.R (line 193, column 64)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/methods-graph.R (line 43, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/clustergraph.R (line 73, column 33)
    • ...
    • R/random.R (line 19, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods-graphAM.R (line 198, column 31)
    • R/MultiGraph.R (line 97, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/methods-graph.R (line 488, column 30)
    • R/TODOT.R (line 33, column 14)
! WARNING: .Deprecated / .Defunct usage (found 5 times)
  • .Defunct() in R/buildDepGraph.R (line 2, column 5)
  • ...
  • .Defunct() in R/methods-graph.R (line 131, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/validGraph.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 72 times)
  • <<- in R/graphNEL.R (line 295, column 33)
  • ...
  • <<- in R/NELhandler.R (line 60, column 20)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/methods-graph.R (line 162, column 38)
  • ...
  • suppressWarnings() in R/zzz.R (line 17, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • graph_handler() (R/gxlReader.R): 169 lines
    • ...
    • _anonymous_.457() (R/methods-graph.R): 78 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/apoptosisGraph.Rd
    • ...
    • man/IMCA.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/attrDataItem-methods.Rd
    • ...
    • man/write.tlp.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • attrDataItem-methods.Rd
    • ...
    • toDotWithRI.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 213 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L17 pars="list")) # ...
    • ...
    • vignettes/MultiGraphClass.Rmd#L310 The operations we have dealt with so
    far ...
ℹ NOTE: Consider 4 spaces instead of tabs; 38 lines (0%) contain tabs.
  First few lines:
    • R/clustergraph.R#L56 out<-rval ...
    • ...
    • R/methods-multiGraph.R#L77 function(object) edgemode(object) == ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2500 lines (26%) are
not.
  First few lines:
    • R/AllClasses.R#L14 representation(nodes="list", # ...
    • ...
    • vignettes/MultiGraphClass.Rmd#L219 to = c("DEN", "IAH", "LAX", " ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 21 NOTES
ℹ See the graph.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.