##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChromHeatMap_1.67.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing ChromHeatMap ─────────────────────────────────────────────────────
✔ Package installed successfully
── ChromHeatMap session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpdAaaF7/file660d81eebae19/ChromHeatMap
→ BiocVersion: 3.24
→ Package: ChromHeatMap
→ PackageVersion: 1.67.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChromHeatMap.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpdAaaF7/file660d81eebae19/ChromHeatMap
→ installDir: /tmp/RtmpdAaaF7/file660d84a682d72
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChromHeatMap ───────────────────────────────────────────
* 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 2.9.0 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:
GeneExpression, CellBiology, Pathways, Survival, GO
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 (64%).
* 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:
    • ChromHeatMap.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ChromHeatMap.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ChromHeatMap...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/makeChrStrandData.R (line 38, column 9)
    • ...
    • require() in R/plotChrMap.R (line 49, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/drawMapDendro.R (line 43, column 24)
    • R/makeChrStrandData.R (line 61, column 13)
    • R/makeChrStrandData.R (line 74, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • chrHeatMap.R (line 107, column 18)
    • ...
    • makeChrStrandData.R (line 87, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/grabChrMapProbes.R (line 26, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/drawMapDendro.R (line 160, column 16)
    • R/paintCytoBands.R (line 127, column 33)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/paintCytoBands.R (line 33, column 17)
    • R/paintCytoBands.R (line 162, column 17)
    • R/plotChrMap.R (line 13, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/chrHeatMap.R (line 24, column 14)
    • ...
    • R/plotChrMap.R (line 83, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • drawMapDendro.R (line 10, column 20)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • drawMapDendro() (R/drawMapDendro.R): 220 lines
    • ...
    • _anonymous_.24() (R/makeChrStrandData.R): 117 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/makeChrStrandData-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • chrNames.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; 72 lines (3%) are > 80 characters long.
  First few lines:
    • R/chrHeatMap.R#L30 start <- min( unlist(lapply(stra ...
    • ...
    • vignettes/ChromHeatMap.Rnw#L99 plotmap<-plotChrMap(chrdata, 1, cytoband
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 568 lines (23%) are
not.
  First few lines:
    • R/chrHeatMap.R#L132 RowSideColors = Ro ...
    • ...
    • vignettes/ChromHeatMap.Rnw#L45 norvegicus}; please contact the mainta ...
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 18 NOTES
ℹ See the ChromHeatMap.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.