##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('gage_2.63.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing gage ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── gage session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpFKj1cO/file1af77e193c3946/gage
→ BiocVersion: 3.24
→ Package: gage
→ PackageVersion: 2.63.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/gage.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpFKj1cO/file1af77e193c3946/gage
→ installDir: /tmp/RtmpFKj1cO/file1af77ed70afc6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gage ───────────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (75%).
* 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:
    • dataPrep.Rnw
    • gage.Rnw
    • RNA-seqWorkflow.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • dataPrep.Rnw
    • gage.Rnw
    • RNA-seqWorkflow.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • dataPrep.Rnw
    • gage.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/dataPrep.Rnw (chunk no. 5, line 64, column 31)
    • ...
    • vignettes/RNA-seqWorkflow.Rnw (chunk no. 14, line 204, column 51)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/dataPrep.Rnw
    • vignettes/gage.Rnw
    • vignettes/RNA-seqWorkflow.Rnw
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/go.gsets.R (line 22, column 11)
    • install() in R/go.gsets.R (line 23, column 20)
* Checking for library/require of gage...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/go.gsets.R (line 19, column 14)
    • require() in R/go.gsets.R (line 24, column 16)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/deComp.R (line 5, column 14)
    • ...
    • R/readList.R (line 4, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • deComp.R (line 30, column 25)
    • ...
    • vennDiagram2.R (line 41, column 20)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/deComp.R (line 53, column 13)
    • ...
    • print() in R/sigGeneSet.R (line 92, column 10)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/deComp.R (line 3, column 11)
    • ...
    • R/sigGeneSet.R (line 76, column 34)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/gagePipe.R (line 21, column 18)
    • R/go.gsets.R (line 26, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 33 times:
    • T in R/deComp.R (line 56, column 41)
    • ...
    • T in R/rownorm.R (line 3, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • esset.grp.R (line 32, column 39)
    • ...
    • kegg.species.code.R (line 10, column 22)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • heatmap2() (R/heatmap2.R): 343 lines
    • ...
    • gagePrep() (R/gagePrep.R): 93 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/gse16873.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gage-internal.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; 213 lines (4%) are > 80 characters long.
  First few lines:
    • R/esset.grp.R#L19 stop("There are less than 1 sign ...
    • ...
    • vignettes/RNA-seqWorkflow.Rnw#L500 The following GAGE and Pathview steps
    re ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/gs.KSTest.R#L56 results[i, ] <- mapply(max, ks.res[1, ] ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 799 lines (15%) are
not.
  First few lines:
    • R/colorpanel.R#L35 ...
    • ...
    • vignettes/RNA-seqWorkflow.Rnw#L399 species = "hsa", o ...
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 | ⚠ 7 WARNINGS | ℹ 17 NOTES
ℹ See the gage.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.