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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SimFFPE_1.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SimFFPE ──────────────────────────────────────────────────────────
✔ Package installed successfully
── SimFFPE session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbCrDF8/file13249a61c01d5b/SimFFPE
→ BiocVersion: 3.24
→ Package: SimFFPE
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SimFFPE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpbCrDF8/file13249a61c01d5b/SimFFPE
→ installDir: /tmp/RtmpbCrDF8/file13249a7e53de35
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SimFFPE ────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpbCrDF8/file13249a61c01d5b/SimFFPE/man/targetReadSimFFPE.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: WholeGenome
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...
* 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 (31%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • SimFFPE.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • SimFFPE.Rnw
* Checking package installation calls in R code...
* Checking for library/require of SimFFPE...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • chimeric_seq_sim_WGS.R (line 26, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/param_estimator.R (line 153, column 18)
    • ...
    • R/readSimFFPE_WGS.R (line 295, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/reads_to_fastq.R (line 73, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/param_estimator.R (line 105, column 17)
* 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:
    • targetReadSimFFPE() (R/readSimFFPE_targeted.R): 380 lines
    • ...
    • calcPhredScoreProfile() (R/param_estimator.R): 130 lines
* Checking man page documentation...
* 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; 19 lines (1%) are > 80 characters long.
  First few lines:
    • R/chimeric_seq_sim_targeted.R#L41 m ...
    • ...
    • vignettes/SimFFPE.Rnw#L202 chromosomes. The different read colors ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 437 lines (16%) are
not.
  First few lines:
    • R/chimeric_seq_modifier.R#L2 target ...
    • ...
    • vignettes/SimFFPE.Rnw#L209 soft-clips are shown as colored vertic ...
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 13 NOTES
ℹ See the SimFFPE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.