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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('viper_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing viper ────────────────────────────────────────────────────────────
✔ Package installed successfully
── viper session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjEM5EN/file152abe4a8d8605/viper
→ BiocVersion: 3.24
→ Package: viper
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/viper.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpjEM5EN/file152abe4a8d8605/viper
→ installDir: /tmp/RtmpjEM5EN/file152abe7f2f1125
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on viper ──────────────────────────────────────────────────
* 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 2.14.0 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...
* 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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* 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 (14%).
* 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:
    • viper.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • viper.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/viper.Rnw (chunk no. 25, line 168, column 85)
    • vignettes/viper.Rnw (chunk no. 27, line 181, column 30)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/viper.Rnw
* Checking package installation calls in R code...
* Checking for library/require of viper...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/aracne.r (line 24, column 19)
    • ...
    • R/viper.r (line 606, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • aracne.r (line 24, column 62)
    • ...
    • viper.r (line 583, column 28)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/msviper.r (line 180, column 10)
    • R/plot.r (line 63, column 21)
    • R/viper.r (line 38, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/general.r (line 139, column 31)
    • ...
    • R/viper.r (line 513, column 38)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/signatureDistance.r (line 28, column 43)
    • R/signatureDistance.r (line 70, column 44)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 7 times:
    • T in R/internal.r (line 444, column 44)
    • ...
    • T in R/viper.r (line 531, column 39)
! WARNING: Remove set.seed usage (found 5 times)
  • set.seed() in R/general.r (line 77, column 17)
  • ...
  • set.seed() in R/viper.r (line 238, 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 20
functions greater than 50 lines.
  The longest 5 functions are:
    • plot.msviper() (R/plot.r): 186 lines
    • ...
    • _anonymous_.236() (R/viper.r): 121 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/msviper-class.Rd
    • man/regulon-class.Rd
    • man/signatureDistance-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • aREA.Rd
  • filterColMatrix.Rd
  • filterRowMatrix.Rd
* Checking package NEWS...
* 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; 655 lines (17%) are > 80 characters long.
  First few lines:
    • R/aracne.r#L3 #' This function generates a regulon obj ...
    • ...
    • vignettes/viper.Rnw#L348 \bibitem{Subramanian2005} Subramanian, A ...
ℹ NOTE: Consider 4 spaces instead of tabs; 101 lines (3%) contain tabs.
  First few lines:
    • R/internal.r#L55 nullpw <- list(eset=sapply(1:per, fun ...
    • ...
    • R/plot.r#L144 densiRes <- densiRes*(tw1[x>=denSte ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 87 lines (2%) are not.
  First few lines:
    • R/aracne.r#L138 adj={ ...
    • ...
    • vignettes/viper.Rnw#L331 \caption{\label{fig:sigviper}Heatmap 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 v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 18 NOTES
ℹ See the viper.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.