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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CNORfeeder_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CNORfeeder ───────────────────────────────────────────────────────
✔ Package installed successfully
── CNORfeeder session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder
→ BiocVersion: 3.24
→ Package: CNORfeeder
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CNORfeeder.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder
→ installDir: /tmp/RtmpNGdquL/file76e1014ca777d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CNORfeeder ─────────────────────────────────────────────
* 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 4.0.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder/man/buildFeederObjectDynamic.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder/man/CNORfeeder-package.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder/man/identifyMisfitIndices.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder/man/integrateLinks.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpNGdquL/file76e1059f44a40/CNORfeeder/man/runDynamicFeeder.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Network,
Bayesian, GraphAndNetwork
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (100%).
* 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:
    • CNORfeeder-vignette.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 23 out of 23 code chunks = 100% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CNORfeeder-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CNORfeeder...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/parEstimationLBodeSSmWeighted.R (line 18, column 7)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Binference.R (line 76, column 15)
    • ...
    • weighting.R (line 101, column 44)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/computeMSE.R (line 188, column 5)
    • ...
    • print() in R/weighting.R (line 58, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Binference.R (line 28, column 17)
    • ...
    • R/weighting.R (line 22, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • F in R/getLBodeContObjFunctionWeighted.R (line 10, column 55)
    • F in R/parEstimationLBodeSSmWeighted.R (line 12, column 78)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Binference.R (line 27, column 22)
    • ...
    • weighting.R (line 21, column 28)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/getLBodeContObjFunctionWeighted.R (line 51, column 7)
* 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 20
functions greater than 50 lines.
  The longest 5 functions are:
    • buildFeederObjectDynamic() (R/buildFeederObjectDynamic.R): 454 lines
    • ...
    • computeMSE() (R/computeMSE.R): 174 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • Binference.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
  Found in files:
    • Binference.Rd
    • mapDDN2model.Rd
    • weighting.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • Binference.Rd
    • mapDDN2model.Rd
    • weighting.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS.Rd
    • CNORfeeder/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; 299 lines (8%) are > 80 characters long.
  First few lines:
    • R/addLinkAND.R#L19 # add a negative and gate to the model ...
    • ...
    • vignettes/CNORfeeder-vignette.Rnw#L510 \newblock OmniPath: guidelines and
    gatew ...
ℹ NOTE: Consider 4 spaces instead of tabs; 251 lines (7%) contain tabs.
  First few lines:
    • R/addLink.R#L27 tmp<-matrix(data=0,nrow=dim(model$int ...
    • ...
    • R/weighting.R#L119 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1180 lines (31%) are
not.
  First few lines:
    • R/addLink.R#L18 ...
    • ...
    • vignettes/CNORfeeder-vignette.Rnw#L509 D. Turei, T. Korcsmaros, J.
    Saez-Rodri ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the CNORfeeder.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.