##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('statTarget_1.43.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing statTarget ───────────────────────────────────────────────────────
✔ Package installed successfully
── statTarget session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmprMFwQf/file147c4a406bff6/statTarget
→ BiocVersion: 3.24
→ Package: statTarget
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/statTarget.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmprMFwQf/file147c4a406bff6/statTarget
→ installDir: /tmp/RtmprMFwQf/file147c4a2b547e86
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on statTarget ─────────────────────────────────────────────
* 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 3.6.0 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...
! WARNING: Invalid BiocViews term(s):
  • 'Machine Learning'
  • 'QC-RFSC'
  • 'ComBat'
* Checking for recommended biocViews...
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 (18%).
* 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: Evaluate more vignette chunks.
ℹ 7 out of 13 code chunks = 53% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Combat.Rmd
    • pathway_analysis.Rmd
    • statTarget.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Combat.Rmd
    • vignettes/pathway_analysis.Rmd
    • vignettes/statTarget.Rmd
* Checking package installation calls in R code...
* Checking for library/require of statTarget...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Cb_qcFree.R (line 31, column 16)
    • ...
    • R/RSDdist.R (line 60, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • aucROC.R (line 15, column 15)
    • ...
    • wmw.R (line 40, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Cb_qcFree.R (line 17, column 5)
    • ...
    • cat() in R/statAnalysis.R (line 322, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/aucROC.R (line 4, column 13)
    • ...
    • R/work_dir.R (line 91, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/RandomF.R (line 65, column 17)
    • R/RandomF.R (line 66, column 17)
    • R/randomForest_ptest.R (line 34, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/shiftCor_combat.R (line 326, column 71)
    • T in R/shiftCor_combat.R (line 351, column 51)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/randomForest_ptest.R (line 88, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressMessages() in R/aucROC.R (line 54, column 30)
  • ...
  • suppressWarnings() in R/showLables_sT.R (line 69, column 21)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 33
functions greater than 50 lines.
  The longest 5 functions are:
    • shiftCor() (R/shiftCor_v2.R): 343 lines
    • ...
    • plsda_stat() (R/plsda_stat.R): 223 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • mdsPlot.Rd
    • predict_RF.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 523 lines (10%) are > 80 characters long.
  First few lines:
    • R/aucROC.R#L1 ### acu.ROC This function provide area u ...
    • ...
    • vignettes/statTarget.Rmd#L349 Luan H., Ji F., Chen Y., Cai Z. (2018) Q
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/shiftCor_combat.R#L347 d <- d.hat[-i] ...
    • ...
    • vignettes/statTarget.Rmd#L122 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 540 lines (10%) are
not.
  First few lines:
    • R/aucROC.R#L54 roc.obj <- suppressMes ...
    • ...
    • vignettes/statTarget.Rmd#L348 ...
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 | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the statTarget.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.