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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MAIT_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MAIT ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── MAIT session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpQGPm39/filecebc72a44f67e/MAIT
→ BiocVersion: 3.24
→ Package: MAIT
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MAIT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpQGPm39/filecebc72a44f67e/MAIT
→ installDir: /tmp/RtmpQGPm39/filecebc77428f9c2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MAIT ───────────────────────────────────────────────────
* 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/RtmpQGPm39/filecebc72a44f67e/MAIT/man/annotateBiotransf.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/classNum.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/FisherLSD.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/inBetween.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/MAIT.FeatureData-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/method.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/pcaLoadings.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/pcaModel.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/pcaScores.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/peakAggregation.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/PLSDA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/plsLoadings.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/plsModel.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/plsScores.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/project.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/removeOnePeakSpectra.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/retrieveSpectrum.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/SearchCand.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/selectK.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/selectPLScomp.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/spectralFUN.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/spectralWilcox.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/successRatio.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/writeExcelTable.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpQGPm39/filecebc72a44f67e/MAIT/man/writeParameterTable.Rd'
* 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: 'Date:' field format is not 'YYYY-MM-DD': 09-06-2020
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • MAIT_Vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • MAIT_Vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MAIT_Vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of MAIT...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/plotPCA.R (line 136, column 5)
    • require() in R/plotPLS.R (line 151, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Biotransformations.R (line 179, column 15)
    • ...
    • R/Biotransformations.R (line 407, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Biotransformations.R (line 195, column 10)
    • ...
    • Validation.R (line 390, column 28)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Biotransformations.R (line 75, column 9)
    • ...
    • cat() in R/Validation.R (line 333, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/computeSpectra.R (line 15, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/identifyMetabolites.R (line 367, column 28)
    • ...
    • R/Validation.R (line 175, column 36)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/peakAnnotation.R (line 208, column 42)
    • R/sampleProcessing.R (line 149, column 13)
    • R/sampleProcessing.R (line 153, column 25)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • getPeaklist-methods.R (line 3, column 43)
    • ...
    • spectralFUN.R (line 73, column 41)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/Biotransformations.Rd
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 22
functions greater than 50 lines.
  The longest 5 functions are:
    • Validation() (R/Validation.R): 404 lines
    • ...
    • sampleProcessing() (R/sampleProcessing.R): 184 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/MAIT.FeatureInfo-class.Rd
  • man/MAIT.PhenoData-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • peakAnnotation.Rd
  • sampleProcessing.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; 904 lines (10%) are > 80 characters long.
  First few lines:
    • R/Biotransformations.R#L1 ######################################## ...
    • ...
    • man/writeParameterTable.Rd#L16 The list of parameters to be printed. Th
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 545 lines (6%) contain tabs.
  First few lines:
    • R/AllClasses.R#L25 ) ...
    • ...
    • man/Validation.Rd#L16 scale=TRUE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1599 lines (18%) are
not.
  First few lines:
    • R/AllClasses.R#L2 representation( ...
    • ...
    • vignettes/MAIT_Vignette.Rnw#L509 peakTolerance=0.005,polari ...
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 | ⚠ 4 WARNINGS | ℹ 21 NOTES
ℹ See the MAIT.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.