##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SRAdb_1.75.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SRAdb ────────────────────────────────────────────────────────────
✔ Package installed successfully
── SRAdb session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfgSgGu/file14708a3daed218/SRAdb
→ BiocVersion: 3.24
→ Package: SRAdb
→ PackageVersion: 1.75.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SRAdb.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpfgSgGu/file14708a3daed218/SRAdb
→ installDir: /tmp/RtmpfgSgGu/file14708af7a8710
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SRAdb ──────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: LongRead,
Network, GraphAndNetwork
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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:
    • SRAdb.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • SRAdb.Rnw
* Checking package installation calls in R code...
* Checking for library/require of SRAdb...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/getSRAinfo.R (line 11, column 9)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • entityGraph.R (line 12, column 18)
    • ...
    • listSRAfile.R (line 30, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/IGVapi.R (line 6, column 3)
    • print() in R/IGVapi.R (line 12, column 3)
    • print() in R/IGVsession.R (line 4, column 30)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ascpSRA.R (line 18, column 18)
    • ...
    • R/startIGV.R (line 13, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/getSRA.R (line 4, column 56)
    • T in R/sraConvert.R (line 7, column 54)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/ascpR.R (line 18, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/entityGraph.R (line 17, column 50)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • sraConvert() (R/sraConvert.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/getFASTQfile.Rd
    • ...
    • man/startIGV.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • ascpR.Rd
    • ...
    • startIGV.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 83% of man
pages use at least one of these tags.
  Found in files:
    • ascpR.Rd
    • ...
    • startIGV.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ascpR.Rd
    • ...
    • startIGV.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; 245 lines (11%) are > 80 characters long.
  First few lines:
    • R/ascpR.R#L2 ## due to complexity with options in asc ...
    • ...
    • vignettes/SRAdb.Rnw#L409 sra_files = getSRAfile( runs, sra_con, f ...
ℹ NOTE: Consider 4 spaces instead of tabs; 446 lines (19%) contain tabs.
  First few lines:
    • R/ascpR.R#L16 for( src in ascpSource ) { ...
    • ...
    • vignettes/SRAdb.Rnw#L415 system ("fastq-dump SRR000648.lite.sra" ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 288 lines (12%) are
not.
  First few lines:
    • R/getFASTQfile.R#L37 return(sraFiles) ...
    • ...
    • vignettes/SRAdb.Rnw#L332 \label{figure:graph} ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the SRAdb.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.