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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('maSigPro_1.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing maSigPro ─────────────────────────────────────────────────────────
✔ Package installed successfully
── maSigPro session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVGdEyH/filecfbd66ead38c3/maSigPro
→ BiocVersion: 3.24
→ Package: maSigPro
→ PackageVersion: 1.85.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/maSigPro.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpVGdEyH/filecfbd66ead38c3/maSigPro
→ installDir: /tmp/RtmpVGdEyH/filecfbd6726c5e3c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on maSigPro ───────────────────────────────────────────────
* 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 2.3.1 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):
  • 'RNA-Seq': Did you meanone of 'DNASeq', 'RNASeq'?
  • 'Differential Expression': Did you mean 'DifferentialExpression'?
* Checking for recommended biocViews...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVGdEyH/filecfbd66ead38c3/maSigPro/man/stepfor.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Regression
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (14%).
* 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:
    • maSigPro.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/maSigPro.Rnw
* Checking package installation calls in R code...
* Checking for library/require of maSigPro...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • average.rows.R (line 9, column 15)
    • ...
    • two.ways.stepfor.R (line 57, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/get.siggenes.R (line 190, column 9)
    • ...
    • print() in R/T.fit.R (line 175, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/IsoModel.R (line 14, column 20)
    • ...
    • R/two.ways.stepfor.R (line 71, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/IsoModel.R (line 39, column 113)
    • T in R/IsoModel.R (line 40, column 50)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/maSigProUsersGuide.R (line 9, column 14)
* Checking parsed R code in R directory, examples, vignettes...
* 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:
    • get.siggenes() (R/get.siggenes.R): 195 lines
    • ...
    • IsoModel() (R/IsoModel.R): 114 lines
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 476 lines (12%) are > 80 characters long.
  First few lines:
    • R/get.siggenes.R#L1 get.siggenes<-function (tstep, rsq = 0.7 ...
    • ...
    • vignettes/maSigPro.Rnw#L42 To obtain the User's Guide you need to i ...
ℹ NOTE: Consider 4 spaces instead of tabs; 66 lines (2%) contain tabs.
  First few lines:
    • R/get.siggenes.R#L103 group.sig <- as.data.frame(group.sig[, ...
    • ...
    • man/seeDS.Rd#L35 Experiment wide Isoform profiles and by ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 920 lines (24%) are
not.
  First few lines:
    • R/get.siggenes.R#L30 matchID.col]), ] ...
    • ...
    • man/two.ways.stepfor.Rd#L64 -1.009, -1.101, -1.014, -0.045, -0.110, ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the maSigPro.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.