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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CMA_1.71.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CMA ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── CMA session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA
→ BiocVersion: 3.24
→ Package: CMA
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CMA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA
→ installDir: /tmp/RtmpUl9Wfp/file76a08227efec0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CMA ────────────────────────────────────────────────────
* 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/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/compare-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/compBoostCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/dldaCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/ElasticNetCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/ElasticNetCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/evaluation-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/fdaCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/fdaCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/flexdaCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/flexdaCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/gbmCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/GeneSelection-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/knnCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/knnCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/LassoCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/Planarplot-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/plot,cloutput-method.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/plrCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/pls_lrCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/pls_rfCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/pnnCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/predoutput-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/qdaCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/rfCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/rfCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/scdaCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/svmCMA-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/svmCMA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/wmc-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/wmc.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUl9Wfp/file76a08e7ddf48/CMA/man/wmcr_result-class.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray
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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • CMA_vignette.rnw
! WARNING: Evaluate more vignette chunks.
ℹ 18 out of 26 code chunks = 69% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • CMA_vignette.rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CMA_vignette.rnw
* Checking package installation calls in R code...
* Checking for library/require of CMA...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/ElasticNetCMA.r (line 27, column 1)
    • ...
    • require() in R/wmc.r (line 29, column 25)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/classes.r (line 432, column 38)
    • ...
    • R/pnnCMA.r (line 49, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classes.r (line 141, column 21)
    • ...
    • wmc.r (line 170, column 54)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/classes.r (line 79, column 11)
    • ...
    • print() in R/classes.r (line 302, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/classes.r (line 266, column 34)
    • ...
    • R/LassoCMA.r (line 58, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/classification.r (line 125, column 37)
    • ...
    • R/evaluation.r (line 233, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/evaluation.r (line 103, column 24)
    • R/wmc.r (line 8, column 38)
    • R/wmc.r (line 11, column 38)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 21 times:
    • F in R/classes.r (line 393, column 78)
    • ...
    • F in R/wmc.r (line 30, column 39)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • classification.r (line 53, column 25)
    • join.r (line 23, column 34)
    • tune.r (line 54, column 25)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/pls_rfCMA.r (line 57, column 1)
  • set.seed() in R/rfCMA.r (line 43, column 25)
  • set.seed() in R/svmCMA.r (line 109, column 1)
* 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 21
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.30() (R/evaluation.r): 222 lines
    • ...
    • _anonymous_.27() (R/classification.r): 152 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/classification-methods.Rd
    • ...
    • man/wmc-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • best.Rd
    • ...
    • wmc.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • classification.Rd
    • ...
    • tune.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • classification.Rd
    • ...
    • tune.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; 896 lines (8%) are > 80 characters long.
  First few lines:
    • R/classes.r#L23 prob="matrix", m ...
    • ...
    • vignettes/CMA_vignette.rnw#L761 comparison <- compare(dalike, plot = TRU
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 696 lines (6%) contain tabs.
  First few lines:
    • R/classes.r#L384 ...
    • ...
    • vignettes/CMA_vignette.rnw#L269 can be tabulated and visualized using t
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3494 lines (31%) are
not.
  First few lines:
    • R/classes.r#L24 ...
    • ...
    • vignettes/CMA_vignette.rnw#L888 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 7 WARNINGS | ℹ 21 NOTES
ℹ See the CMA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.