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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cmapR_1.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing cmapR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── cmapR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpadLXRF/file76a0b7a0c1e42/cmapR
→ BiocVersion: 3.24
→ Package: cmapR
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/cmapR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpadLXRF/file76a0b7a0c1e42/cmapR
→ installDir: /tmp/RtmpadLXRF/file76a0b63d66dcf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cmapR ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Network
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...
* Checking License: for restrictive use...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* 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...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • tutorial.Rmd
✖ ERROR: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/tutorial.Rmd (chunk no. 1, line 30, column 5)
    • vignettes/tutorial.Rmd (chunk no. 1, line 32, column 14)
! WARNING: Potential package installation calls found in vignette(s)
  Found in files:
    • vignettes/tutorial.Rmd (chunk no. 1, line 30, column 5)
* Checking package installation calls in R code...
* Checking for library/require of cmapR...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/io.R (line 349, column 3)
    • ...
    • cat() in R/io.R (line 409, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/GCT.R (line 181, column 32)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/GCT.R (line 139, column 34)
    • ...
    • R/utils.R (line 564, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • T in R/GCT.R (line 74, column 33)
    • ...
    • T in R/utils.R (line 467, column 59)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • utils.R (line 828, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/io.R (line 35, column 29)
  • ...
  • suppressMessages() in R/io.R (line 830, column 27)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/GCT.R): 210 lines
    • ...
    • _anonymous_.43() (R/utils.R): 65 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • update_gctx.Rd
  • ...
  • write_tbl.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • update_gctx.Rd
    • ...
    • write_tbl.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • update_gctx.Rd
    • ...
    • write_tbl.Rd
* 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; 26 lines (1%) are > 80 characters long.
  First few lines:
    • R/utils.R#L872 # slice out the rows that only have ...
    • ...
    • vignettes/tutorial.Rmd#L290 The `GCT` class is quite similar in spir ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/GCT.R#L169 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 974 lines (33%) are
not.
  First few lines:
    • R/deprecated.R#L10 warning("parse.gctx has been deprecate ...
    • ...
    • vignettes/tutorial.Rmd#L269 main="score vs. rank") ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the cmapR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.