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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CGEN_3.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CGEN ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── CGEN session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplIXiLN/file648d61760691c/CGEN
→ BiocVersion: 3.24
→ Package: CGEN
→ PackageVersion: 3.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CGEN.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplIXiLN/file648d61760691c/CGEN
→ installDir: /tmp/RtmplIXiLN/file648d6319af6f9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CGEN ───────────────────────────────────────────────────
* 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 4.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmplIXiLN/file648d61760691c/CGEN/man/CGEN.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG,
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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:
    • vignette_GxE.Rnw
    • vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • vignette_GxE.Rnw
    • vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CGEN...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getMatchedSets.R (line 135, column 54)
    • ...
    • R/snp_matched.R (line 246, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • additive.test.R (line 73, column 29)
    • ...
    • wga.R (line 1087, column 34)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/additive.test.R (line 28, column 5)
    • ...
    • print() in R/wga.R (line 1255, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getMatchedSets.R (line 260, column 22)
    • ...
    • R/wga_plot.R (line 768, column 30)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getMatchedSets.R (line 82, column 49)
    • ...
    • R/wga.R (line 869, column 44)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/additive.test.R (line 19, column 42)
    • ...
    • R/wga.R (line 1248, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/source.SCORE.functions.R (line 3838, column 13)
    • T in R/source.SCORE.functions.R (line 3840, column 15)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/wga_read.R (line 983, column 12)
    • system() in R/wga_util.R (line 2628, column 12)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/wga_plot.R (line 1041, column 16)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Avoid 'Sys.setenv' (found 1 times)
  • Sys.setenv() in R/wga_plot.R (line 1091, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 193
functions greater than 50 lines.
  The longest 5 functions are:
    • snp.main.additiveTrend() (R/wga_GbyE.R): 1614 lines
    • ...
    • scoreTest.small.logit5.max.indep6()
    (R/R_scoreTest.small.logit5.max.indep6.r): 738 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/LocusMapData.Rd
    • man/Xdata.Rd
    • man/Xdata2.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • snp.list.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • snp.list.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; 2181 lines (6%) are > 80 characters long.
  First few lines:
    • R/additive.test.R#L5 additive.test <- function(data, response ...
    • ...
    • vignettes/vignette.Rnw#L112 getWaldTest(fit$HCL, c( "BRCA.status" , ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1768 lines (5%) contain tabs.
  First few lines:
    • R/getMatchedSets.R#L15 if(is.data.frame(x)) ...
    • ...
    • vignettes/vignette.Rnw#L82 strata.var = Xdata$ethnic.group, size ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 16360 lines (44%) are
not.
  First few lines:
    • R/additive.test.R#L6 strata.var=NULL, op=NU ...
    • ...
    • vignettes/vignette.Rnw#L102 cc.var="CCStrat", n ...
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 | ⚠ 6 WARNINGS | ℹ 21 NOTES
ℹ See the CGEN.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.