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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('iCNV_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing iCNV ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── iCNV session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV
→ BiocVersion: 3.24
→ Package: iCNV
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/iCNV.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV
→ installDir: /tmp/RtmpN8ki5q/fileb334d2ddf2263
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on iCNV ───────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.3.1 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...
* Checking for recommended biocViews...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/chr.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/filenm.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/icnv_res0.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_baf.chr.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_baf.id.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_baf.nm.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_baf.pos.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_baf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_plr.pos.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/ngs_plr.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/normObj.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/projname.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/qcObj.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/sampname_qc.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/sampname.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/snp_baf.pos.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/snp_baf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/snp_lrr.pos.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpN8ki5q/fileb334d3b4e7c1b/iCNV/man/snp_lrr.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
ExperimentalDesign, Normalization, QualityControl
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 (8%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • iCNV-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of iCNV...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/bambaf_from_vcf.R (line 77, column 5)
    • ...
    • cat() in R/plotindi_function.R (line 151, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bambaf_from_vcf.R (line 24, column 17)
    • ...
    • R/plotindi_function.R (line 31, column 44)
* 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 9
functions greater than 50 lines.
  The longest 5 functions are:
    • HMMiEM() (R/iCNV_detection_function.R): 322 lines
    • ...
    • exactCNi() (R/iCNV_detection_function.R): 82 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/normObj.Rd
    • man/qcObj.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; 169 lines (7%) are > 80 characters long.
  First few lines:
    • R/bambaf_from_vcf.R#L6 #' ngs_baf.nm: name of the bamfiles; ngs ...
    • ...
    • vignettes/iCNV-vignette.Rmd#L357 projname=pr ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • R/plot_intensity.R#L18 stopifnot(is.numeric(chr)) ...
    • ...
    • R/plot_intensity.R#L24 xlab=paste0('chr',chr),ylab='sample ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 891 lines (39%) are
not.
  First few lines:
    • R/iCNV_detection_function.R#L45 stopifnot(is.numeric(maxIt)) ...
    • ...
    • vignettes/iCNV-vignette.Rmd#L357 projname=pr ...
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 | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the iCNV.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.