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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('fishpond_2.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing fishpond ─────────────────────────────────────────────────────────
✔ Package installed successfully
── fishpond session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYQdkdU/file1ad63f5c7b4d67/fishpond
→ BiocVersion: 3.24
→ Package: fishpond
→ PackageVersion: 2.19.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/fishpond.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYQdkdU/file1ad63f5c7b4d67/fishpond
→ installDir: /tmp/RtmpYQdkdU/file1ad63f4c58cde8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on fishpond ───────────────────────────────────────────────
* 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (38%).
* 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:
    • allelic.Rmd
    • swish.Rmd
* Checking package installation calls in R code...
* Checking for library/require of fishpond...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/alevin-EC.R (line 208, column 23)
    • ...
    • R/salmon-EC.R (line 189, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • helper-allelic.R (line 488, column 21)
    • ...
    • pair.R (line 26, column 52)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/alevin-loadFry.R (line 141, column 20)
    • ...
    • R/alevin-loadFry.R (line 441, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/alevin-EC.R (line 55, column 10)
    • ...
    • R/swish.R (line 403, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/helper-allelic.R (line 533, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • plotAllelicGene() (R/helper-allelic.R): 267 lines
    • ...
    • importAllelicCounts() (R/helper-allelic.R): 134 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addStatsFromCSV.Rd
    • ...
    • splitSwish.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • makeTx2Tss.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • makeTx2Tss.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; 60 lines (1%) are > 80 characters long.
  First few lines:
    • R/alevin-EC.R#L32 #' identifiers followed by an underscore ...
    • ...
    • vignettes/swish.Rmd#L763 [Orchestrating Single-Cell Analysis with ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1661 lines (29%) are
not.
  First few lines:
    • R/alevin-EC.R#L47 ignoreAfterBar = FA ...
    • ...
    • vignettes/swish.Rmd#L1157 text(1:(2*n), rep(i,2*n), id.perms, co ...
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 | ⚠ 0 WARNINGS | ℹ 14 NOTES
ℹ See the fishpond.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.