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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cn.farms_1.61.0.tar.gz','quit-with-status'=TRUE)"
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── Installing cn.farms ─────────────────────────────────────────────────────────
✔ Package installed successfully
── cn.farms session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpcyWMEw/file76a121034edf4/cn.farms
→ BiocVersion: 3.24
→ Package: cn.farms
→ PackageVersion: 1.61.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/cn.farms.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpcyWMEw/file76a121034edf4/cn.farms
→ installDir: /tmp/RtmpcyWMEw/file76a12152c5dbf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cn.farms ───────────────────────────────────────────────
* 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 3.0 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/RtmpcyWMEw/file76a121034edf4/cn.farms/vignettes/cn.farms.Rnw'
* 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (55%).
* 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:
    • cn.farms.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • cn.farms.Rnw
* Checking package installation calls in R code...
* Checking for library/require of cn.farms...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/createAnnotation.R (line 71, column 9)
    • require() in R/sFinit.R (line 194, column 12)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/callSummarize.R (line 231, column 5)
    • ...
    • R/sFsnowWrappers.R (line 199, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • callSummarize.R (line 185, column 14)
    • ...
    • windowFunctions.R (line 133, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/callSummarize.R (line 28, column 5)
    • ...
    • print() in R/windowFunctions.R (line 71, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/callSummarize.R (line 37, column 33)
    • ...
    • R/sFinit.R (line 749, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/createAnnotation.R (line 67, column 22)
    • ...
    • R/summarizationSl.R (line 141, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/sFclusterFunctions.R (line 103, column 22)
    • ...
    • R/snowfallExt.R (line 132, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 7 times:
    • T in R/distributionDistance.R (line 28, column 25)
    • ...
    • F in R/normalizeProbeSequence.R (line 141, column 50)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/distributionDistance.R (line 52, column 17)
  • set.seed() in R/sFsnowWrappers.R (line 259, column 5)
  • set.seed() in R/sFsnowWrappers.R (line 271, column 5)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Remove browser() statements (found 1 times)
  • browser() in R/normalizeSor.R (line 46, column 5)
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/plotDendrogram.R (line 21, column 15)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 59 times)
  • suppressWarnings() in R/callSummarize.R (line 169, column 5)
  • ...
  • suppressWarnings() in R/summarizationSl.R (line 122, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 39
functions greater than 50 lines.
  The longest 5 functions are:
    • summarizeFarmsExact3() (R/summarizeFarmsLaplaceExact3.R): 527 lines
    • ...
    • summarizeFarmsVariational() (R/summarizeFarmsLaplaceVar.R): 329 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • cn.farms.Rd
    • ...
    • summarizeFarmsStatistics.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
  Found in files:
    • cn.farms.Rd
    • ...
    • normalizeNpData.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cn.farms.Rd
    • ...
    • normalizeNpData.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; 353 lines (3%) are > 80 characters long.
  First few lines:
    • R/callSummarize.R#L170 suppressWarnings(sfExport("summarize ...
    • ...
    • vignettes/cn.farms.Rnw#L662 10:00:19 | Annotation directory: /tmp ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1490 lines (13%) contain tabs.
  First few lines:
    • R/createAnnotation.R#L31 annotDir = NULL, checks = TRUE) { ...
    • ...
    • vignettes/cn.farms.Rnw#L305 smoothing=FALSE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1231 lines (10%) are
not.
  First few lines:
    • R/cnFarms.R#L21 ...
    • ...
    • vignettes/cn.farms.Rnw#L776 chrom start end man_fsetid ...
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 | ⚠ 5 WARNINGS | ℹ 21 NOTES
ℹ See the cn.farms.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.