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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('qpgraph_2.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing qpgraph ──────────────────────────────────────────────────────────
✔ Package installed successfully
── qpgraph session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpORrsJA/file10502224957c56/qpgraph
→ BiocVersion: 3.24
→ Package: qpgraph
→ PackageVersion: 2.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/qpgraph.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpORrsJA/file10502224957c56/qpgraph
→ installDir: /tmp/RtmpORrsJA/file10502254db958c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on qpgraph ────────────────────────────────────────────────
* 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 3.5 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: GeneTarget,
Network
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 (65%).
* 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:
    • eQTLnetworks.Rnw
    • qpgraphSimulate.Rnw
    • qpTxRegNet.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • qpTxRegNet.Rnw
* Checking package installation calls in R code...
* Checking for library/require of qpgraph...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/eQTLnetworkEstimationParam-methods.R (line 99, column 45)
    • ...
    • require() in R/qpgraph.R (line 3927, column 24)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/eQTLcross-methods.R (line 117, column 39)
    • ...
    • R/qpgraph.R (line 4708, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllClass.R (line 6, column 40)
    • ...
    • UGgmm-methods.R (line 191, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/eQTLnetwork-methods.R (line 620, column 33)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/eQTLnetwork-methods.R (line 718, column 21)
    • ...
    • R/qpSimulate.R (line 283, column 32)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/qpCItest.R (line 1362, column 10)
    • ...
    • R/qpgraph.R (line 2270, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/qpgraph.R (line 4791, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 13 times:
    • T in R/qpgraph.R (line 2343, column 5)
    • ...
    • T in R/qpgraph.R (line 3545, column 21)
* 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 57
functions greater than 50 lines.
  The longest 5 functions are:
    • .eQTLplotHive() (R/eQTLnetwork-methods.R): 1811 lines
    • ...
    • qpTopPairs() (R/qpgraph.R): 220 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/eQTLnetworkEstimate.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • eQTLcross-class.Rd
    • ...
    • UGgmm-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • qpAvgNrr.Rd
    • ...
    • qpUpdateCliquesRemoving.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • qpAvgNrr.Rd
    • ...
    • qpUpdateCliquesRemoving.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; 1975 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClass.R#L40 ## class erMarkedGraphParam to hold para ...
    • ...
    • vignettes/qpTxRegNet.Rnw#L536 \caption{Reverse-engineered transcriptio
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1653 lines (9%) contain tabs.
  First few lines:
    • R/eQTLnetwork-methods.R#L533 id2=id2, ...
    • ...
    • R/eQTLnetwork-methods.R#L2361 } # closing brace, this is the end! ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 5694 lines (31%) are
not.
  First few lines:
    • R/AllClass.R#L3 representation(p="integer", ...
    • ...
    • vignettes/qpTxRegNet.Rnw#L531 annotation="org.EcK12.eg.d ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the qpgraph.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.