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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('debrowser_1.41.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing debrowser ────────────────────────────────────────────────────────
✔ Package installed successfully
── debrowser session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfONWig/file7e72d39afc2f8/debrowser
→ BiocVersion: 3.24
→ Package: debrowser
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/debrowser.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpfONWig/file7e72d39afc2f8/debrowser
→ installDir: /tmp/RtmpfONWig/file7e72d4f7a2989
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on debrowser ──────────────────────────────────────────────
* 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: 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...
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • rmarkdown
! WARNING: Evaluate more vignette chunks.
ℹ 1 out of 2 code chunks = 50% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DEBrowser.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/DEBrowser.Rmd
* Checking package installation calls in R code...
* Checking for library/require of debrowser...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/funcs.R (line 587, column 47)
    • ...
    • library() in R/ui.R (line 20, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dataLoad.R (line 23, column 41)
    • ...
    • R/prepdata.R (line 193, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • all2all.R (line 87, column 22)
    • ...
    • uifuncs.R (line 522, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/dataLoad.R (line 99, column 13)
    • ...
    • print() in R/server.R (line 657, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/batcheffect.R (line 230, column 17)
    • ...
    • R/uifuncs.R (line 594, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/funcs.R (line 588, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 11 times:
    • T in R/batcheffect.R (line 131, column 39)
    • ...
    • F in R/mainScatter.R (line 344, column 49)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/funcs.R (line 587, column 13)
  • suppressMessages() in R/funcs.R (line 587, column 30)
* 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:
    • deServer() (R/server.R): 578 lines
    • ...
    • _anonymous_.322() (R/condSelect.R): 102 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/actionButtonDE.Rd
    • ...
    • man/togglePanels.Rd



##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
No methods found in package ‘DOSE’ for request: ‘summary’ when loading ‘debrowser’
* 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; 628 lines (7%) are > 80 characters long.
  First few lines:
    • R/barmain.R#L21 cols = ...
    • ...
    • vignettes/DEBrowser.Rmd#L1116 15. Johnson et al. (2007) Adjusting batc
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 95 lines (1%) contain tabs.
  First few lines:
    • R/condSelect.R#L479 getMetaSelector <- function(metadata = N ...
    • ...
    • vignettes/DEBrowser.Rmd#L1081 https://debrowser.umassmed.edu/?jsonobj ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 657 lines (7%) are
not.
  First few lines:
    • R/all2all.R#L18 cex=2) ...
    • ...
    • vignettes/DEBrowser.Rmd#L883 ...
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 debrowser.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.