##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('isobar_1.59.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing isobar ───────────────────────────────────────────────────────────
✔ Package installed successfully
── isobar session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsQ1nAR/filec5eaf10113122/isobar
→ BiocVersion: 3.24
→ Package: isobar
→ PackageVersion: 1.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/isobar.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsQ1nAR/filec5eaf10113122/isobar
→ installDir: /tmp/RtmpsQ1nAR/filec5eaf1c1988cc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on isobar ─────────────────────────────────────────────────
* 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...
! WARNING: Invalid BiocViews term(s):
  • 'Bioinformatics'
  • 'MultipleComparisons': Did you mean 'MultipleComparison'?
* Checking for recommended biocViews...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpsQ1nAR/filec5eaf10113122/isobar/man/subsetIBSpectra.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Normalization,
Preprocessing
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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:
    • isobar-devel.Rnw
    • ...
    • isobar.Rnw
Warning: ! in callr subprocess.
Caused by error in `parse(text = code, keep.source = FALSE)`:
! <text>:1:8: unexpected '<'
1: alist( <
           ^
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • isobar-devel.Rnw
    • isobar-ptm.Rnw
    • isobar.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/isobar.Rnw (chunk no. 26, line 241, column 25)
    • vignettes/isobar.Rnw (chunk no. 29, line 274, column 79)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/isobar-ptm.Rnw
    • vignettes/isobar-usecases.Rnw
* Checking package installation calls in R code...
* Checking for library/require of isobar...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/distr-methods.R (line 22, column 15)
    • ...
    • R/utils.R (line 210, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • distr-methods.R (line 74, column 13)
    • ...
    • report-utils.R (line 714, column 46)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/metareport-utils.R (line 132, column 3)
    • ...
    • print() in R/sharedpep-methods.R (line 120, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/IBSpectra-class.R (line 833, column 24)
    • ...
    • R/utils.R (line 258, column 78)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/IBSpectra-class.R (line 673, column 10)
    • ...
    • R/utils.R (line 46, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/isobar-import.R (line 745, column 10)
    • ...
    • R/utils.R (line 270, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 35 times:
    • T in R/IBSpectra-class.R (line 681, column 28)
    • ...
    • T in R/sharedpep-methods.R (line 90, column 39)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ratio-methods.R (line 1135, column 17)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/metareport-utils.R (line 111, column 3)
    • ...
    • system() in R/utils.R (line 269, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/isobar-log.Rd
ℹ Found @ in vignettes/isobar-ptm.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 6 times)
  • <<- in R/isobar-import.R (line 48, column 21)
  • ...
  • <<- in R/report-utils.R (line 575, column 29)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 49
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.147() (R/ratio-methods.R): 205 lines
    • ...
    • write.xls.report() (R/report-utils-xls.R): 155 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/maplot.protein.Rd
  • man/Tlsd-class.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/specificities.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/calc.startpos.Rd
    • ...
    • man/writeIBSpectra.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calc.delta.score.Rd
    • ...
    • writeIBSpectra.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:
    • getPtmInfo.Rd
    • proteinInfo-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getPtmInfo.Rd
    • proteinInfo-methods.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; 1432 lines (10%) are > 80 characters long.
  First few lines:
    • R/distr-methods.R#L4 calcProbXDiffNormals <- function(X,mu_Y, ...
    • ...
    • vignettes/isobar.Rnw#L801 \texttt{mascotParser2.pl} coverts from M ...
ℹ NOTE: Consider 4 spaces instead of tabs; 142 lines (1%) contain tabs.
  First few lines:
    • R/distr-methods.R#L10 return(rep(NA,seq_along(mu_Y))) ...
    • ...
    • man/ratio-summ.Rd#L98 'data.frame': 11 variables: ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 6127 lines (42%) are
not.
  First few lines:
    • R/distr-methods.R#L5 # calculates a vector of either P(X>=Y ...
    • ...
    • vignettes/isobar.Rnw#L819 toLatex(sessionInfo()) ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 7 WARNINGS | ℹ 23 NOTES
ℹ See the isobar.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.