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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SBGNview_1.27.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing SBGNview ─────────────────────────────────────────────────────────
✔ Package installed successfully
── SBGNview session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpewLMjW/file128b5c6715f189/SBGNview
→ BiocVersion: 3.24
→ Package: SBGNview
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SBGNview.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpewLMjW/file128b5c6715f189/SBGNview
→ installDir: /tmp/RtmpewLMjW/file128b5c7197ff4a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SBGNview ───────────────────────────────────────────────
* 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 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: KEGG
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 (24%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • pathway.enrichment.analysis.Rmd
    • SBGNview.quick.start.Rmd
    • SBGNview.Vignette.Rmd
✖ ERROR: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/pathway.enrichment.analysis.Rmd (chunk no. 3, line 80, column
    16)
* Checking package installation calls in R code...
* Checking for library/require of SBGNview...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/mapping.utilities.R (line 345, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/color.panel.R (line 206, column 9)
    • ...
    • print() in R/SBGN.to.SVG.R (line 314, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/download.utilities.R (line 136, column 74)
    • ...
    • R/SBGNview.R (line 155, column 77)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 19 times:
    • T in R/download.utilities.R (line 359, column 83)
    • ...
    • T in R/mapping.utilities.R (line 262, column 69)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/SBGNview.R (line 150, column 9)
* 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 43
functions greater than 50 lines.
  The longest 5 functions are:
    • findPathways() (R/download.utilities.R): 373 lines
    • ...
    • parse.glyph() (R/parsing.utilities.R): 138 lines
* Checking man page documentation...

##############################################################################
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).
##############################################################################
##############################################################################
SBGNview 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.

Users are required to formally cite the SBGNview paper and Pathview paper (not
just mention them) in publications or products. For details, do
'citation("SBGNview"); citation("Pathview")' within R.
##############################################################################
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • highlightArcs.Rd
    • ...
    • renderSbgn.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 30% of man
pages use at least one of these tags.
  Found in files:
    • highlightArcs.Rd
    • ...
    • renderSbgn.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • highlightArcs.Rd
    • ...
    • renderSbgn.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; 1889 lines (21%) are > 80 characters long.
  First few lines:
    • R/color.panel.R#L2 ######################################## ...
    • ...
    • vignettes/SBGNview.Vignette.Rmd#L563 ```{r , eval = FALSE, echo =
    TRUE,result ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1110 lines (13%) are
not.
  First few lines:
    • R/color.panel.R#L122 "Link to SBGN notation ...
    • ...
    • vignettes/SBGNview.Vignette.Rmd#L573 ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the SBGNview.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.