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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('pathview_1.52.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing pathview ─────────────────────────────────────────────────────────
✔ Package installed successfully
── pathview session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfgajIv/file8687d7f31e9ad/pathview
→ BiocVersion: 3.23
→ Package: pathview
→ PackageVersion: 1.52.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/pathview.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpfgajIv/file8687d7f31e9ad/pathview
→ installDir: /tmp/RtmpfgajIv/file8687d917b3ec
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pathview ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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: GeneTarget,
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 that Package field matches directory/tarball name...
* 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 (50%).
* 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:
    • pathview.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • pathview.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • pathview.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/pathview.Rnw (chunk no. 15, line 102, column 76)
    • ...
    • vignettes/pathview.Rnw (chunk no. 36, line 348, column 74)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/pathview.Rnw
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/geneannot.map.R (line 17, column 18)
    • install() in R/sim.mol.data.R (line 70, column 24)
* Checking for library/require of pathview...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/combineKEGGnodes.R (line 16, column 15)
    • ...
    • R/subtypeDisplay.kedge.R (line 13, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • circles.R (line 8, column 12)
    • ...
    • strfit.R (line 45, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/geneannot.map.R (line 59, column 9)
    • print() in R/keggview.graph.R (line 52, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/circles.R (line 4, column 4)
    • ...
    • R/zzz.R (line 16, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/geneannot.map.R (line 19, column 22)
    • ...
    • R/subtypeDisplay.kedge.R (line 23, column 29)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/combineKEGGnodes.R (line 27, column 15)
    • ...
    • R/pathview.R (line 233, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 55 times:
    • T in R/col.key.R (line 19, column 21)
    • ...
    • F in R/sim.mol.data.R (line 27, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • download.kegg.R (line 39, column 32)
    • ...
    • pathview.R (line 215, column 27)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/sim.mol.data.R (line 5, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/download.kegg.R (line 53, column 20)
  • suppressWarnings() in R/geneannot.map.R (line 46, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • keggview.graph() (R/keggview.graph.R): 365 lines
    • ...
    • sim.mol.data() (R/sim.mol.data.R): 107 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/pathview-internal.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).
##############################################################################
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • combineKEGGnodes.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; 272 lines (6%) are > 80 characters long.
  First few lines:
    • R/col.key.R#L2 function(discrete=FALSE, limit=1.0, bi ...
    • ...
    • vignettes/pathview.Rnw#L629 \item \textbf{Special Note}: some KEGG x ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1664 lines (35%) are
not.
  First few lines:
    • R/circles.R#L3 theta <- seq(0, 2 * pi, length=n) ...
    • ...
    • vignettes/pathview.Rnw#L586 species = "ko", out.s ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the pathview.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.