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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('clippda_1.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing clippda ──────────────────────────────────────────────────────────
✔ Package installed successfully
── clippda session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpX5b3Qt/file7117c13f52f53/clippda
→ BiocVersion: 3.24
→ Package: clippda
→ PackageVersion: 1.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/clippda.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpX5b3Qt/file7117c13f52f53/clippda
→ installDir: /tmp/RtmpX5b3Qt/file7117c5c993c44
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on clippda ────────────────────────────────────────────────
* 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 2.13.1 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/RtmpX5b3Qt/file7117c13f52f53/clippda/man/checkNo.replicates.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/fisherInformation.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/liverRawData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/mostSimilarTwo.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/pheno_urine.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/preProcRepeatedPeakData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/proteomicsExprsData-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/proteomicsExprsData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/replicateCorrelations-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/replicateCorrelations.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/sampleSize.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/sampleSize3DscatterPlots.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/sampleSizeContourPlots.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/sampleSizeParameters-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/sampleSizeParameters.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/show-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/spectrumFilter.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/man/ZvaluesfrommultinomPlots.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpX5b3Qt/file7117c13f52f53/clippda/vignettes/clippda.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, Microarray, MassSpectrometry, Metabolomics, Epigenetics,
Cheminformatics, Transcriptomics, Normalization, Bayesian, Clustering,
Regression, ExonArray, GeneExpression, RNASeq, TwoChannel, MicroRNAArray,
mRNAMicroarray, ProprietaryPlatforms, CellBiology, BiomedicalInformatics,
FunctionalGenomics, SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialSplicing, GeneSetEnrichment, BatchEffect, QualityControl,
TimeCourse, DataImport
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • clippda.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • clippda.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • clippda.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/clippda.Rnw
* Checking package installation calls in R code...
* Checking for library/require of clippda...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/replicateCorrelations.Generic.R (line 43, column 1)
    • ...
    • library() in R/ZvaluesfrommultinomPlots.R (line 92, column 2)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • betweensampleVariance.Generic.R (line 27, column 15)
    • ...
    • spectrumFilter.R (line 14, column 10)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ZvaluesfrommultinomPlots.R (line 103, column 1)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/betweensampleVariance.Generic.R (line 12, column 15)
    • ...
    • R/ZvaluesfrommultinomPlots.R (line 107, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/aclinicalProteomicsData-methods.Rd
ℹ Found @ in man/betweensampleVariance.Rd
ℹ Found @ in man/clippda-package.Rd
ℹ Found @ in man/fisherInformation.Rd
ℹ Found @ in man/phenoDataFrame.Rd
ℹ Found @ in man/proteomicsExprsData.Rd
ℹ Found @ in man/proteomicspData.Rd
ℹ Found @ in man/replicateCorrelations.Rd
ℹ Found @ in man/sample_technicalVariance.Rd
ℹ Found @ in man/sampleSize.Rd
ℹ Found @ in man/sampleSizeParameters.Rd
ℹ Found @ in vignettes/clippda.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • sampleSizeContourPlots() (R/sampleSizeContourPlots.R): 297 lines
    • ...
    • _anonymous_.10() (R/fisherInformation.Generic.R): 93 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/aclinicalProteomicsData-methods.Rd
    • ...
    • man/show-methods.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; 624 lines (12%) are > 80 characters long.
  First few lines:
    • R/aclinicalProteomicData.class.R#L1
    setClass("aclinicalProteomicsData",repre ...
    • ...
    • vignettes/clippda.Rnw#L777 sampleSize3DscatterPlots(Z,m,DIFF,VAR,be ...
ℹ NOTE: Consider 4 spaces instead of tabs; 25 lines (0%) contain tabs.
  First few lines:
    • R/aclinicalProteomicData.methods.R#L4 cat("Type :", class(object), "\n")
    ...
    • ...
    • man/pheno_urine.Rd#L14 the sample class} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 349 lines (7%) are
not.
  First few lines:
    • R/checkNo.replicates.R#L15 if(dim(rawData[rawData$SampleTag = ...
    • ...
    • vignettes/clippda.Rnw#L713 early-cancer (SELDI - blue, MALDI - red ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the clippda.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.