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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('NetSAM_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing NetSAM ───────────────────────────────────────────────────────────
✔ Package installed successfully
── NetSAM session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0gIW7J/filef70259387558/NetSAM
→ BiocVersion: 3.24
→ Package: NetSAM
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/NetSAM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0gIW7J/filef70259387558/NetSAM
→ installDir: /tmp/Rtmp0gIW7J/filef702512d5321f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on NetSAM ─────────────────────────────────────────────────
* 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 3.0.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
✖ ERROR: No biocViews terms found.
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: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (15%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • NetSAM.Rmd
! WARNING: BiocInstaller code found in vignette(s)
  Found in files:
    • c("vignettes/NetSAM.Rmd (chunk no. 2, line 85, column 1)",
    "vignettes/NetSAM.Rmd (chunk no. 2, line 86, column 1)")
✖ ERROR: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/NetSAM.Rmd (chunk no. 2, line 78, column 1)
    • ...
    • vignettes/NetSAM.Rmd (chunk no. 2, line 88, column 1)
! WARNING: Potential package installation calls found in vignette(s)
  Found in files:
    • vignettes/NetSAM.Rmd (chunk no. 2, line 78, column 1)
    • ...
    • vignettes/NetSAM.Rmd (chunk no. 2, line 88, column 1)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/NetSAM.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/Rtmp0gIW7J/filef70259387558/NetSAM/vignettes/NetSAM.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
  Found in files:
    • vignettes/NetSAM.Rmd
* Checking package installation calls in R code...
* Checking for library/require of NetSAM...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • consensusNet.R (line 22, column 19)
    • ...
    • testFileFormat.R (line 176, column 38)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • featureAssociation.R (line 106, column 26)
    • ...
    • NetSAM.R (line 975, column 29)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/consensusNet.R (line 75, column 3)
    • ...
    • cat() in R/testFileFormat.R (line 41, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/GOAssociation.R (line 198, column 40)
    • ...
    • R/NetAnalyzer.R (line 201, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/mapToSymbol.R (line 39, column 26)
    • ...
    • R/testFileFormat.R (line 166, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 188 times:
    • F in R/featureAssociation.R (line 58, column 153)
    • ...
    • F in R/NetSAM.R (line 1003, column 42)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17 times)
  • suppressWarnings() in R/featureAssociation.R (line 277, column 13)
  • ...
  • suppressWarnings() in R/testFileFormat.R (line 149, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • MatSAM() (R/MatSAM.R): 350 lines
    • ...
    • NetAnalyzer() (R/NetAnalyzer.R): 162 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/consensusNet.Rd
    • man/mapToSymbol.Rd
    • man/MatNet.Rd

* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 733 lines (15%) are > 80 characters long.
  First few lines:
    • R/consensusNet.R#L1 consensusNet <- function(data, organism= ...
    • ...
    • vignettes/NetSAM.Rmd#L577 "`ouputType`" to "`top`" and "`topNum`" ...
ℹ NOTE: Consider 4 spaces instead of tabs; 355 lines (7%) contain tabs.
  First few lines:
    • R/mapToSymbol.R#L154 sctM <- mapresult$sct_symb ...
    • ...
    • man/testFileFormat.Rd#L45 formatedData <- testFileFormat(inputMat ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 806 lines (16%) are
not.
  First few lines:
    • R/consensusNet.R#L2 nMatNet=2, nThr ...
    • ...
    • vignettes/NetSAM.Rmd#L579 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 5 WARNINGS | ℹ 16 NOTES
ℹ See the NetSAM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.