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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MultiDataSet_1.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MultiDataSet ─────────────────────────────────────────────────────
✔ Package installed successfully
── MultiDataSet session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp31TDB4/filef31b350be76ab/MultiDataSet
→ BiocVersion: 3.24
→ Package: MultiDataSet
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MultiDataSet.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp31TDB4/filef31b350be76ab/MultiDataSet
→ installDir: /tmp/Rtmp31TDB4/filef31b3566d56b8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MultiDataSet ───────────────────────────────────────────
* 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 4.1 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: RNASeq
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (58%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MultiDataSet_Extending_Proteome.Rmd
    • vignettes/MultiDataSet.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MultiDataSet...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/MultiDataSet-add_eset.R (line 72, column 25)
    • ...
    • R/ResultSet-show.R (line 14, column 76)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • downloadGEO.R (line 30, column 22)
    • ...
    • ResultSet-plot.R (line 57, column 50)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • conversionFunctions.R (line 22, column 24)
    • ...
    • ResultSet-varLabels.R (line 8, column 32)
* 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 8
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/MultiDataset-subseting.R): 178 lines
    • ...
    • definition() (R/ResultSet-plot.R): 72 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • mae2mds.Rd
  • ...
  • w_mcia.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; 265 lines (10%) are > 80 characters long.
  First few lines:
    • R/1_MultiDataSet-ClassGenerics.R#L4 #' datasets in form of triplets
    (assayDa ...
    • ...
    • vignettes/MultiDataSet.Rmd#L259 With this line of code, we can select al
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 45 lines (2%) contain tabs.
  First few lines:
    • R/downloadGEO.R#L15 # #' gse_list = c("GSE40576", "GSE61989 ...
    • ...
    • vignettes/MultiDataSet_Extending_Proteome.Rmd#L25 LoD.B = c(1.6461E+05,
    2.8121E+04, 2. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 181 lines (7%) are
not.
  First few lines:
    • R/1_MultiDataSet-ClassGenerics.R#L24 Class = "MultiDataSet", ...
    • ...
    • vignettes/MultiDataSet.Rmd#L36 ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the MultiDataSet.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.