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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('crlmm_1.71.0.tar.gz','quit-with-status'=TRUE)"
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── Installing crlmm ────────────────────────────────────────────────────────────
✔ Package installed successfully
── crlmm session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvPessR/file7b4ac67d80207/crlmm
→ BiocVersion: 3.24
→ Package: crlmm
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/crlmm.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvPessR/file7b4ac67d80207/crlmm
→ installDir: /tmp/RtmpvPessR/file7b4ac3f1f2aaa
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on crlmm ──────────────────────────────────────────────────
* 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 2.14.0 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/RtmpvPessR/file7b4ac67d80207/crlmm/man/ABpanel.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/celfile-utils.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/cnrmaAffy.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/constructAffyCNSet.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/genotypeAffy.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/genotypeInf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/genotypes.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/ListClassConstructors.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/plotSNPs.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/posteriorProbability.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/predictionRegion.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/preprocessInf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/man/validCdfNames.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/vignettes/CopyNumberOverview.Rnw'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/vignettes/IlluminaPreprocessCN.Rnw'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvPessR/file7b4ac67d80207/crlmm/vignettes/Infrastructure.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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (32%).
* 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:
    • AffyGW.Rnw
    • ...
    • Infrastructure.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/AffyGW.Rnw
    • ...
    • vignettes/Infrastructure.Rnw
* Checking package installation calls in R code...
* Checking for library/require of crlmm...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/cnrma-functions.R (line 27, column 13)
    • ...
    • require() in R/test_crlmm_package.R (line 23, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cnrma-functions.R (line 4, column 42)
    • ...
    • R/methods-CNSet.R (line 743, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cnrma-functions.R (line 149, column 54)
    • ...
    • plot.R (line 42, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cnrma-functions.R (line 2614, column 17)
    • ...
    • cat() in R/test_crlmm_package.R (line 44, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cnrma-functions.R (line 80, column 19)
    • ...
    • R/plot.R (line 39, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/cnrma-functions.R (line 986, column 25)
    • ...
    • R/crlmm-illumina.R (line 1375, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cnrma-functions.R (line 742, column 25)
    • R/cnrma-functions.R (line 1205, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 7 times:
    • T in R/cnrma-functions.R (line 740, column 49)
    • ...
    • F in R/krlmm.R (line 967, column 49)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • krlmm.R (line 524, column 19)
    • ...
    • krlmm.R (line 1079, column 97)
! WARNING: Remove set.seed usage (found 6 times)
  • set.seed() in R/cnrma-functions.R (line 244, column 9)
  • ...
  • set.seed() in R/snprma-functions.R (line 208, column 3)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Defunct() in R/cnrma-functions.R (line 409, column 9)
  • .Defunct() in R/cnrma-functions.R (line 2068, column 9)
  • .Defunct() in R/methods-CNSetLM.R (line 2, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/cnrma-functions.R (line 416, column 14)
  • ...
  • suppressWarnings() in R/krlmm.R (line 475, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 42
functions greater than 50 lines.
  The longest 5 functions are:
    • crlmmGT2() (R/crlmmGT2.R): 278 lines
    • ...
    • crlmmGT() (R/crlmm-functions.R): 167 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/posteriorProbability.Rd
  • man/predictionRegion.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AssayData-methods.Rd
    • man/CNSet-methods.Rd
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • ABpanel.Rd
    • ...
    • snprmaAffy.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 26% of man
pages use at least one of these tags.
  Found in files:
    • calculateRBaf.Rd
    • ...
    • xyplot.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • calculateRBaf.Rd
    • ...
    • xyplot.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 547 lines (6%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L2 ##setGeneric("getParam", function(object ...
    • ...
    • vignettes/IlluminaPreprocessCN.Rnw#L1 %\VignetteIndexEntry{Preprocessing
    and g ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4758 lines (55%) contain tabs.
  First few lines:
    • R/AllGenerics.R#L99 standardGeneric("posteriorProbabilit ...
    • ...
    • crlmm/NAMESPACE#L98 BafLrrSetList) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 874 lines (10%) are
not.
  First few lines:
    • R/cnrma-functions.R#L1037 } ...
    • ...
    • vignettes/genotyping.Rnw#L65 representation as it saves a significa ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 7 WARNINGS | ℹ 19 NOTES
ℹ See the crlmm.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.