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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scde_2.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scde ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── scde session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfaxQtg/file12a81441838dc/scde
→ BiocVersion: 3.24
→ Package: scde
→ PackageVersion: 2.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scde.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpfaxQtg/file12a81441838dc/scde
→ installDir: /tmp/RtmpfaxQtg/file12a81440a3bcd2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scde ───────────────────────────────────────────────────
* 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 3.0.0 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, SingleCell, PrincipalComponent
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • diffexp.Rmd
    • pagoda.Rmd
✖ ERROR: No 'VignetteEngine' specified in vignette.
  Add 'VignetteEngine' to the following files:
    • vignettes/diffexp.Rmd
    • vignettes/pagoda.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • diffexp.Rmd
    • pagoda.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • diffexp.Rmd
    • pagoda.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/diffexp.Rmd
    • vignettes/pagoda.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scde...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/functions.R (line 496, column 9)
    • ...
    • require() in R/functions.R (line 3538, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/functions.R (line 4138, column 21)
    • R/functions.R (line 4175, column 21)
    • R/functions.R (line 4223, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • functions.R (line 541, column 29)
    • ...
    • functions.R (line 6161, column 91)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • functions.R (line 4919, column 40)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/functions.R (line 1129, column 21)
    • ...
    • R/functions.R (line 5787, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/functions.R (line 980, column 27)
    • ...
    • R/functions.R (line 4007, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/functions.R (line 305, column 14)
    • ...
    • R/functions.R (line 5721, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • functions.R (line 977, column 27)
    • ...
    • functions.R (line 3502, column 39)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/functions.R (line 2102, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 38 times)
  • <<- in R/functions.R (line 5001, column 24)
  • ...
  • <<- in R/functions.R (line 6005, column 18)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/functions.R (line 5079, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • pagoda.varnorm() (R/functions.R): 465 lines
    • ...
    • calculate.individual.models() (R/functions.R): 195 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/es.mef.small.Rd
    • ...
    • man/scde.edff.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/papply.Rd
now dyn.unload("/tmp/RtmpfaxQtg/file12a81440a3bcd2/lib/scde/libs/scde.so") ...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • clean.gos.Rd
  • ...
  • show.app.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 47% of man
pages use at least one of these tags.
  Found in files:
    • clean.gos.Rd
    • ...
    • show.app.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; 1237 lines (18%) are > 80 characters long.
  First few lines:
    • R/functions.R#L1 ##' Single-cell Differential Expression ...
    • ...
    • vignettes/pagoda.Rmd#L221 Now we can go through the same analysis ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 460 lines (7%) are
not.
  First few lines:
    • R/functions.R#L91 go.env <- as.list(go.env) ...
    • ...
    • vignettes/diffexp.Rmd#L246 })) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 7 WARNINGS | ℹ 22 NOTES
ℹ See the scde.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.