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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('EGSEA_1.41.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing EGSEA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── EGSEA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5LCtgt/file86aa45d40c7eb/EGSEA
→ BiocVersion: 3.24
→ Package: EGSEA
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/EGSEA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5LCtgt/file86aa45d40c7eb/EGSEA
→ installDir: /tmp/Rtmp5LCtgt/file86aa418ccebe2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EGSEA ──────────────────────────────────────────────────
* 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 4.3.0 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/Rtmp5LCtgt/file86aa45d40c7eb/EGSEA/vignettes/EGSEA.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...
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 (35%).
* 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:
    • EGSEA.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • EGSEA.Rnw
* Checking package installation calls in R code...
* Checking for library/require of EGSEA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/EGSEAclass.R (line 277, column 27)
    • ...
    • R/idxAnno.R (line 715, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • EGSEAclass.R (line 224, column 43)
    • ...
    • wrapperUtils.R (line 106, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/egseaAux.R (line 137, column 9)
    • ...
    • print() in R/idxAnno.R (line 660, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/egseaAux.R (line 133, column 15)
    • ...
    • R/wrapperUtils.R (line 107, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/egseaUtils.R (line 49, column 18)
    • ...
    • R/wrapperUtils.R (line 14, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/EGSEAclass.R (line 237, column 32)
    • ...
    • R/gsaplots.R (line 210, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 10 times)
  • suppressWarnings() in R/EGSEAclass.R (line 658, column 31)
  • ...
  • suppressMessages() in R/gsaplots.R (line 641, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 27
functions greater than 50 lines.
  The longest 5 functions are:
    • egsea.main() (R/egseaUtils.R): 214 lines
    • ...
    • writeEGSEAResultsToHTML() (R/htmlUtils.R): 151 lines
* Checking man page documentation...

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################





* Checking package NEWS...
* 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; 429 lines (5%) are > 80 characters long.
  First few lines:
    • R/arraydata.R#L4 #' @description This is dataset is provi ...
    • ...
    • vignettes/EGSEA.Rnw#L1010 <<echo=TRUE, eval=TRUE, tidy=TRUE, tidy. ...
ℹ NOTE: Consider 4 spaces instead of tabs; 34 lines (0%) contain tabs.
  First few lines:
    • R/egseaMain.R#L285 #' display.top = 5, sort.by="avg.rank ...
    • ...
    • vignettes/EGSEA.Rnw#L966 report.dir="./il13-egsea-ora-re ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1155 lines (14%) are
not.
  First few lines:
    • R/EGSEAclass.R#L84 ...
    • ...
    • vignettes/EGSEA.Rnw#L966 report.dir="./il13-egsea-ora-re ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the EGSEA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.