##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ENmix_1.49.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing ENmix ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ENmix session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5oXHAM/file876f959a4a21f/ENmix
→ BiocVersion: 3.24
→ Package: ENmix
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ENmix.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5oXHAM/file876f959a4a21f/ENmix
→ installDir: /tmp/Rtmp5oXHAM/file876f95dc2bd8c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ENmix ──────────────────────────────────────────────────
* 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 3.5.0 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...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (42%).
* 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 23 out of 24 code chunks = 95% unevaluated
ℹ 
* Checking package installation calls in R code...
* Checking for library/require of ENmix...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/estimateCellProp.R (line 15, column 3)
    • ...
    • require() in R/readmanifest.R (line 102, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/DMR_finding.R (line 27, column 17)
    • ...
    • R/utils.R (line 47, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calcdetP.R (line 35, column 15)
    • ...
    • utils.R (line 81, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/ctrlsva.R (line 27, column 5)
    • ...
    • print() in R/readidat.R (line 64, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/calcdetP.R (line 16, column 12)
    • ...
    • R/utils.R (line 85, column 26)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/readidat.R (line 49, column 46)
    • R/readidat.R (line 110, column 46)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/mage_norm_function.R (line 80, column 56)
    • ...
    • R/readidat.R (line 110, column 53)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 27 times:
    • T in R/DunedinPACE.R (line 63, column 34)
    • ...
    • F in R/p.qqplot.R (line 8, column 68)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • dupicc.R (line 57, column 26)
    • ...
    • readmanifest.R (line 9, column 28)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/readmanifest.R (line 2, column 25)
    • ...
    • system() in R/readmanifest.R (line 9, column 57)
! WARNING: Remove set.seed usage (found 6 times)
  • set.seed() in R/mage_norm_function.R (line 93, column 1)
  • ...
  • set.seed() in R/methyAge.R (line 53, column 1)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/methscore.R (line 91, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 28
functions greater than 50 lines.
  The longest 5 functions are:
    • methscore() (R/methscore.R): 555 lines
    • ...
    • QCinfo() (R/QCinfo.R): 200 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/combp.Rd
    • ...
    • man/predSex.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • B2M.Rd
    • ...
    • simubed.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 95% of man
pages use at least one of these tags.
  Found in files:
    • B2M.Rd
    • ...
    • simubed.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; 525 lines (7%) are > 80 characters long.
  First few lines:
    • R/calcdetP.R#L5 stop("[QCinfo] The input should be ...
    • ...
    • vignettes/ENmix.Rmd#L893 analyzing, grouping and correcting spati ...
ℹ NOTE: Consider 4 spaces instead of tabs; 47 lines (1%) contain tabs.
  First few lines:
    • R/dupicc.R#L10 if(is.null(qc)){stop("Please provide EN ...
    • ...
    • man/methscore.Rd#L52 Higgins-Chen et al. \emph{A computationa ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1236 lines (16%) are
not.
  First few lines:
    • R/calcdetP.R#L5 stop("[QCinfo] The input should be ...
    • ...
    • vignettes/ENmix.Rmd#L878 package for the analysis of Infinium DN ...
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 | ⚠ 6 WARNINGS | ℹ 18 NOTES
ℹ See the ENmix.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.