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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('IHW_1.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing IHW ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── IHW session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKb0MoI/file2ca8887f7aff2b/IHW
→ BiocVersion: 3.24
→ Package: IHW
→ PackageVersion: 1.41.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/IHW.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKb0MoI/file2ca8887f7aff2b/IHW
→ installDir: /tmp/RtmpKb0MoI/file2ca8885187f88a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on IHW ────────────────────────────────────────────────────
* 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 3.3.0 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...
* 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 (40%).
* 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:
    • introduction_to_ihw.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/introduction_to_ihw.Rmd
* Checking package installation calls in R code...
* Checking for library/require of IHW...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/helpers.R (line 79, column 9)
    • ...
    • R/ihw_convex.R (line 1049, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • helpers.R (line 68, column 32)
    • ...
    • ihw_convex.R (line 984, column 57)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ihw_class.R (line 361, column 3)
    • print() in R/ihw_convex.R (line 995, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ihw_convex.R (line 720, column 22)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ihw_convex.R (line 344, column 37)
    • R/ihw_convex.R (line 730, column 29)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/helpers.R (line 23, column 5)
  • set.seed() in R/ihw_convex.R (line 224, column 17)
  • set.seed() in R/ihw_convex.R (line 328, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/helpers.R (line 22, column 29)
  • <<- in R/ihw_convex.R (line 223, column 41)
  • <<- in R/ihw_convex.R (line 327, column 41)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • ihw_milp() (R/ihw_convex.R): 349 lines
    • ...
    • ihw_internal() (R/ihw_convex.R): 144 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • ihw.DESeqResults.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ihw.DESeqResults.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 255 lines (12%) are > 80 characters long.
  First few lines:
    • R/helpers.R#L3 #' Hypotheses are stratified into nbins ...
    • ...
    • vignettes/introduction_to_ihw.Rmd#L338 ```{r compareihw2, fig.width = 3,
    fig.he ...
ℹ NOTE: Consider 4 spaces instead of tabs; 758 lines (36%) contain tabs.
  First few lines:
    • R/helpers.R#L25 rfs <- rank(covariate, ties.method=ties ...
    • ...
    • R/weights.R#L47 ws <- (1-lambda)*ws + lambda*mean(ws) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 233 lines (11%) are
not.
  First few lines:
    • R/helpers.R#L18 if (!is.null(seed) && ties.method=="ra ...
    • ...
    • vignettes/introduction_to_ihw.Rmd#L340 xlim = c(0, 0.1), ylim = c(0, 0.1)
    ...
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 20 NOTES
ℹ See the IHW.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.