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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('diffGeneAnalysis_1.95.0.tar.gz','quit-with-status'=TRUE)"
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── Installing diffGeneAnalysis ─────────────────────────────────────────────────
✔ Package installed successfully
── diffGeneAnalysis session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpUr9lrm/file827941265d9b0/diffGeneAnalysis
→ BiocVersion: 3.24
→ Package: diffGeneAnalysis
→ PackageVersion: 1.95.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/diffGeneAnalysis.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUr9lrm/file827941265d9b0/diffGeneAnalysis
→ installDir: /tmp/RtmpUr9lrm/file8279423c8588c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on diffGeneAnalysis ───────────────────────────────────────
* 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/RtmpUr9lrm/file827941265d9b0/diffGeneAnalysis/man/assocAnalysis.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUr9lrm/file827941265d9b0/diffGeneAnalysis/man/biasAdjust.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUr9lrm/file827941265d9b0/diffGeneAnalysis/man/dataTrim.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUr9lrm/file827941265d9b0/diffGeneAnalysis/man/refGroup.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Normalization
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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • diffGeneAnalysis.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • diffGeneAnalysis.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/diffGeneAnalysis.Rnw
* Checking package installation calls in R code...
* Checking for library/require of diffGeneAnalysis...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • assocAnalysis.R (line 29, column 11)
    • ...
    • refGroup.R (line 48, column 11)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/assocAnalysis.R (line 20, column 2)
    • ...
    • print() in R/refGroup.R (line 61, column 2)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/assocAnalysis.R (line 32, column 11)
    • ...
    • R/assocAnalysis.R (line 46, column 16)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/curveFit.R (line 91, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/curveFit.R (line 15, column 3)
  • ...
  • suppressWarnings() in R/refGroup.R (line 20, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.2() (R/curveFit.R): 142 lines
    • ...
    • _anonymous_.2() (R/assocAnalysis.R): 61 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • assocAnalysis.Rd
    • ...
    • refGroup.Rd
* 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; 41 lines (4%) are > 80 characters long.
  First few lines:
    • R/assocAnalysis.R#L2 function(bAdjusted,numSlides,ctrl,exp,sd ...
    • ...
    • vignettes/diffGeneAnalysis.Rnw#L158 (ii) Knowlton N,Dozmorov I, Centola
    M.  ...
ℹ NOTE: Consider 4 spaces instead of tabs; 39 lines (4%) contain tabs.
  First few lines:
    • vignettes/diffGeneAnalysis.Rnw#L24 (i) DGAP is used on the raw gene
    intens ...
    • ...
    • vignettes/diffGeneAnalysis.Rnw#L148 (xvi) Open results.csv created in the
    " ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 548 lines (52%) are
not.
  First few lines:
    • R/assocAnalysis.R#L3 e<-ctrl+1 ...
    • ...
    • vignettes/diffGeneAnalysis.Rnw#L159 Bioonformatics.2004 Dec
    12;20(18):3687- ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the diffGeneAnalysis.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.