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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('codelink_1.81.0.tar.gz','quit-with-status'=TRUE)"
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── Installing codelink ─────────────────────────────────────────────────────────
✔ Package installed successfully
── codelink session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNbHVUj/file779e668d2a4e9/codelink
→ BiocVersion: 3.24
→ Package: codelink
→ PackageVersion: 1.81.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/codelink.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNbHVUj/file779e668d2a4e9/codelink
→ installDir: /tmp/RtmpNbHVUj/file779e61517264e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on codelink ───────────────────────────────────────────────
* 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 2.10 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/RtmpNbHVUj/file779e668d2a4e9/codelink/man/codPlot.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, Metabolomics, Proteomics, Epigenetics, Cheminformatics,
Transcriptomics, Normalization, Bayesian, Clustering, Regression, ExonArray,
GeneExpression, RNASeq, TwoChannel, MicroRNAArray, mRNAMicroarray,
ProprietaryPlatforms, CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, ImmunoOncology, AlternativeSplicing, DifferentialExpression,
DifferentialSplicing, GeneSetEnrichment, BatchEffect, MultipleComparison,
QualityControl, TimeCourse
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (80%).
* 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:
    • Codelink_Introduction.Rnw
    • Codelink_Legacy.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Codelink_Introduction.Rnw
    • Codelink_Legacy.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Codelink_Legacy.Rnw
* Checking package installation calls in R code...
* Checking for library/require of codelink...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/filter.R (line 77, column 19)
    • R/filter.R (line 83, column 19)
    • R/filter.R (line 91, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Codelink-class.R (line 26, column 33)
    • ...
    • plot.R (line 714, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Codelink-class.R (line 27, column 25)
    • ...
    • print() in R/Codelink-class.R (line 53, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CodelinkSet-methods.R (line 6, column 11)
    • ...
    • R/plot.R (line 576, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/file.R (line 170, column 30)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/filter.R (line 109, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/file.R (line 27, column 62)
    • F in R/file.R (line 5, column 36)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • CodelinkSet-tools.R (line 41, column 23)
    • CodelinkSet-tools.R (line 91, column 26)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Deprecated() in R/data.R (line 54, column 9)
  • .Deprecated() in R/file.R (line 87, column 9)
  • .Deprecated() in R/norm.R (line 7, column 9)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • .readCodelinkRaw() (R/file.R): 371 lines
    • ...
    • plotDensities() (R/plot.R): 72 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/arrayNew.Rd
    • ...
    • man/writeCodelink.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • arrayNew.Rd
    • ...
    • writeCodelink.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 56% of man
pages use at least one of these tags.
  Found in files:
    • arrayNew.Rd
    • ...
    • writeCodelink.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • arrayNew.Rd
    • ...
    • writeCodelink.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; 160 lines (3%) are > 80 characters long.
  First few lines:
    • R/cluster.R#L70 write.table(mat, file = file, quote = F ...
    • ...
    • vignettes/Codelink_Legacy.Rnw#L288 The function \Rfunction{writeCodelink}
    e ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2094 lines (46%) contain tabs.
  First few lines:
    • R/cluster.R#L3 standardGeneric("writeCluster")) ...
    • ...
    • man/SNR.Rd#L8 SNR(Smean, Bmedian, Bstdev) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 209 lines (5%) are
not.
  First few lines:
    • R/file.R#L518 w=createTypeWeights(object,type.weight ...
    • ...
    • man/writeCodelink.Rd#L17 \item{chip}{chip package to use, norma ...
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 | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the codelink.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.