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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('R3CPET_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing R3CPET ───────────────────────────────────────────────────────────
✔ Package installed successfully
── R3CPET session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBHszBP/file1069b760362f48/R3CPET
→ BiocVersion: 3.24
→ Package: R3CPET
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/R3CPET.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpBHszBP/file1069b760362f48/R3CPET
→ installDir: /tmp/RtmpBHszBP/file1069b72cfa58ce
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on R3CPET ─────────────────────────────────────────────────
* 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 3.2 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/RtmpBHszBP/file1069b760362f48/R3CPET/man/EntrezToHGNC.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpBHszBP/file1069b760362f48/R3CPET/man/getRegionsInNetwork-methods.Rd'
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
✖ ERROR: Remove whitespace from DESCRIPTION field names.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • R3CPET.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • R3CPET.Rnw
* Checking package installation calls in R code...
* Checking for library/require of R3CPET...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/ChromMaintainers-methods.r (line 443, column 23)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ChiapetExperimentData-methods.r (line 239, column 27)
    • ...
    • R/NetworkCollection-methods.r (line 5, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ChiapetExperimentData-methods.r (line 65, column 18)
    • ...
    • NetworkCollection-methods.r (line 160, column 61)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ChiapetExperimentData-methods.r (line 283, column 3)
    • ...
    • print() in R/NetworkCollection-methods.r (line 147, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ChiapetExperimentData-methods.r (line 42, column 12)
    • ...
    • R/NetworkCollection-methods.r (line 47, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ChiapetExperimentData-methods.r (line 66, column 10)
    • ...
    • R/PrepareData.r (line 26, column 20)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ChiapetExperimentData-methods.r (line 525, column 27)
    • ...
    • R/DAVIDQuery.r (line 110, column 21)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ChiapetExperimentData-methods.r (line 6, column 17)
    • ...
    • DAVIDQuery.r (line 136, column 45)
* 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:
    • .DAVIDQuery() (R/DAVIDQuery.r): 93 lines
    • _anonymous_.399() (R/ChromMaintainers-methods.r): 55 lines
    • .createBEDFile.Centered() (R/helpers-utils.R): 55 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/Biogrid.Rd
    • ...
    • man/RPKMS.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • ChiapetExperimentData-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 60% of man
pages use at least one of these tags.
  Found in files:
    • annotateExpression-methods.Rd
    • ...
    • visualizeInteractions-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annotateExpression-methods.Rd
    • ...
    • visualizeInteractions-methods.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; 646 lines (13%) are > 80 characters long.
  First few lines:
    • R/AllClasses.r#L19 prototype= prototype(networks=N ...
    • ...
    • vignettes/R3CPET.Rnw#L458 For example, Figure 5. shows a screensho ...
ℹ NOTE: Consider 4 spaces instead of tabs; 115 lines (2%) contain tabs.
  First few lines:
    • R/ChiapetExperimentData-methods.r#L222
    V(PPI)[!is.na(pos)]$RPKM<-RPKM[pos[! ...
    • ...
    • vignettes/R3CPET.Rnw#L450 \item statistics selection option : in ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1495 lines (30%) are
not.
  First few lines:
    • R/AllClasses.r#L4 representation( ...
    • ...
    • vignettes/R3CPET.Rnw#L447 ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the R3CPET.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.