##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('spikeLI_2.73.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing spikeLI ──────────────────────────────────────────────────────────
✔ Package installed successfully
── spikeLI session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiyHHgi/file14566558503313/spikeLI
→ BiocVersion: 3.24
→ Package: spikeLI
→ PackageVersion: 2.73.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/spikeLI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpiyHHgi/file14566558503313/spikeLI
→ installDir: /tmp/RtmpiyHHgi/file1456654e1044f8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spikeLI ────────────────────────────────────────────────
* 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...
* 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...
* 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • spikeLI.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/spikeLI.Rnw
* Checking package installation calls in R code...
* Checking for library/require of spikeLI...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • collapse.R (line 28, column 38)
    • ...
    • IvsDG.R (line 166, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/collapse.R (line 7, column 5)
    • ...
    • cat() in R/IvsDG.R (line 168, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/collapse.R (line 87, column 23)
    • ...
    • R/IvsDG.R (line 135, column 39)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/collapse.R (line 18, column 17)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.2() (R/collapse.R): 263 lines
    • IvsDG() (R/IvsDG.R): 170 lines
    • Ivsc() (R/Ivsc.R): 89 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/collapse.Rd
    • man/Ivsc.Rd
    • man/IvsDG.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; 115 lines (9%) are > 80 characters long.
  First few lines:
    • R/collapse.R#L11 cat("\nSPIKE_INA does not exits, ple ...
    • ...
    • man/spikeLI.package.Rd#L42 \code{\link{collapse}}, \code{\link{Iv ...
ℹ NOTE: Consider 4 spaces instead of tabs; 17 lines (1%) contain tabs.
  First few lines:
    • R/collapse.R#L27 if (nbGenes>4){ ...
    • ...
    • R/IvsDG.R#L135 if(length(conctot)==0) conctot=1.e-10 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 132 lines (10%) are
not.
  First few lines:
    • R/collapse.R#L231 text(xPM[txt ...
    • ...
    • vignettes/spikeLI.Rnw#L347 \bibinfo{pages}{14719} (\bibinfo{year} ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 14 NOTES
ℹ See the spikeLI.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.