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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('pcaMethods_2.4.0.tar.gz','quit-with-status'=TRUE)"
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── Installing pcaMethods ───────────────────────────────────────────────────────
✔ Package installed successfully
── pcaMethods session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYqMJlJ/file86aad31a58e66/pcaMethods
→ BiocVersion: 3.23
→ Package: pcaMethods
→ PackageVersion: 2.4.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/pcaMethods.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpYqMJlJ/file86aad31a58e66/pcaMethods
→ installDir: /tmp/RtmpYqMJlJ/file86aad5d05b8e3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pcaMethods ─────────────────────────────────────────────
* 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...
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* 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:
    • missingValues.Rnw
    • outliers.Rnw
    • pcaMethods.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • missingValues.Rnw
    • outliers.Rnw
    • pcaMethods.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/pcaMethods.Rnw (chunk no. 1, line 11, column 46)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/missingValues.Rnw
    • vignettes/outliers.Rnw
    • vignettes/pcaMethods.Rnw
* Checking package installation calls in R code...
* Checking for library/require of pcaMethods...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/nlpca.R (line 113, column 15)
    • ...
    • R/xval.R (line 271, column 7)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • BPCA_dostep.R (line 34, column 15)
    • ...
    • xval.R (line 282, column 29)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • errorHierarchic.R (line 45, column 35)
    • xval.R (line 232, column 51)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/bpca.R (line 133, column 9)
    • ...
    • cat() in R/svdImpute.R (line 94, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/kEstimate.R (line 156, column 22)
    • ...
    • R/nipalsPca.R (line 93, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/pca.R (line 193, column 10)
    • R/prep.R (line 81, column 13)
    • R/xval.R (line 228, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/checkData.R (line 40, column 15)
    • ...
    • R/optiAlgCgd.R (line 67, column 12)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 11 times:
    • T in R/BPCA_dostep.R (line 25, column 5)
    • ...
    • T in R/BPCA_dostep.R (line 71, column 64)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/ppca.R (line 79, column 5)
  • set.seed() in R/xval.R (line 273, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/pca.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/AllClasses.R (line 300, column 13)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/xval.R (line 113, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
  The longest 5 functions are:
    • kEstimate() (R/kEstimate.R): 173 lines
    • ...
    • Q2() (R/xval.R): 123 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/helix.Rd
    • man/metaboliteData.Rd
    • man/metaboliteDataComplete.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/pcaMethods-deprecated.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • asExprSet.Rd
    • ...
    • showNniRes.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; 115 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L6 setGeneric("DModX", function(object, dat ...
    • ...
    • vignettes/pcaMethods.Rnw#L506 {\sl Missing value estimation for DNA mi
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (0%) contain tabs.
  First few lines:
    • R/AllClasses.R#L189 scores="matrix", ...
    • ...
    • vignettes/pcaMethods.Rnw#L360 deliver better results than BPCA and Ni ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1439 lines (26%) are
not.
  First few lines:
    • R/AllClasses.R#L83 representation(net="matrix", ...
    • ...
    • vignettes/pcaMethods.Rnw#L484 Walther D., and Selbig J. {\sl pcaMeth ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the pcaMethods.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.