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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('npGSEA_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing npGSEA ───────────────────────────────────────────────────────────
✔ Package installed successfully
── npGSEA session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA
→ BiocVersion: 3.24
→ Package: npGSEA
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/npGSEA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA
→ installDir: /tmp/Rtmp5vUEwK/filef8a8a14807d2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on npGSEA ─────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/alphaValue-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/betaValue-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/geneSetName-methods.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/npGSEA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/npGSEAResultChiSq-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/npGSEAResultNorm-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/npGSEAResultNormCollection-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp5vUEwK/filef8a8a707eb6f0/npGSEA/man/zStat-methods.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, GO, KEGG, 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2015-5-6
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • npGSEA.Rnw
* Checking package installation calls in R code...
* Checking for library/require of npGSEA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllClasses.R (line 18, column 18)
    • R/AllClasses.R (line 47, column 18)
    • R/AllClasses.R (line 73, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • miscDataPrepFunctions.R (line 95, column 27)
    • ...
    • miscFunctions.R (line 200, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/miscFunctions.R (line 141, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/miscDataPrepFunctions.R (line 35, column 13)
    • ...
    • R/miscFunctions.R (line 219, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/miscDataPrepFunctions.R (line 55, column 15)
    • ...
    • R/miscDataPrepFunctions.R (line 98, column 31)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • getIncidence.R (line 12, column 19)
    • npGSEA.R (line 19, column 16)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • npGSEA() (R/npGSEA.R): 82 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/alphaValue-methods.Rd
    • ...
    • man/zStat-methods.Rd
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
* 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; 202 lines (8%) are > 80 characters long.
  First few lines:
    • R/getIncidence.R#L3 ##' getIncidence returns an incidence ve ...
    • ...
    • vignettes/npGSEA.Rnw#L485 Larson and Owen.  (2015).  Moment based ...
ℹ NOTE: Consider 4 spaces instead of tabs; 71 lines (3%) contain tabs.
  First few lines:
    • R/miscDataPrepFunctions.R#L12 sdx <- sd(xg, na.rm=TRUE) ...
    • ...
    • vignettes/npGSEA.Rnw#L286 res7_wts ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 92 lines (4%) are not.
  First few lines:
    • R/AllClasses.R#L54 } ...
    • ...
    • vignettes/npGSEA.Rnw#L404 ...
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 | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the npGSEA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.