##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SWATH2stats_1.43.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SWATH2stats ──────────────────────────────────────────────────────
✔ Package installed successfully
── SWATH2stats session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6wubl3/file1493d04c92a6b8/SWATH2stats
→ BiocVersion: 3.24
→ Package: SWATH2stats
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SWATH2stats.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp6wubl3/file1493d04c92a6b8/SWATH2stats
→ installDir: /tmp/Rtmp6wubl3/file1493d045bfe268
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SWATH2stats ────────────────────────────────────────────
* 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 2.10.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (10%).
* 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:
    • SWATH2stats_vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • SWATH2stats_example_script.Rmd
    • SWATH2stats_vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/SWATH2stats_vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of SWATH2stats...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plot_correlation_between_samples.R (line 92, column 5)
    • ...
    • print() in R/sample_annotation.R (line 117, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/mscore4assayfdr.R (line 49, column 27)
    • R/mscore4pepfdr.R (line 49, column 27)
    • R/mscore4protfdr.R (line 53, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/assess_fdr_byrun.R (line 142, column 13)
    • ...
    • R/validate_columns.R (line 42, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/convert_protein_ids.R (line 101, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • assess_fdr_byrun() (R/assess_fdr_byrun.R): 111 lines
    • ...
    • plot_variation_vs_total() (R/plot_variation_vs_total.R): 83 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/MSstats_data.Rd
    • ...
    • man/Study_design.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • convert_protein_ids.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • convert_protein_ids.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • convert_protein_ids.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; 344 lines (9%) are > 80 characters long.
  First few lines:
    • R/assess_decoy_rate.R#L37 message("Number of non-decoy identif ...
    • ...
    • vignettes/SWATH2stats_vignette.Rnw#L527 Venable J.D., et al. (2004).
    Automated a ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 301 lines (8%) are
not.
  First few lines:
    • R/assess_decoy_rate.R#L25 column = " ...
    • ...
    • vignettes/SWATH2stats_vignette.Rnw#L526 \\ ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the SWATH2stats.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.