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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('NOISeq_2.57.0.tar.gz','quit-with-status'=TRUE)"
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── Installing NOISeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── NOISeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmphEfwHH/filef7ccd70171003/NOISeq
→ BiocVersion: 3.24
→ Package: NOISeq
→ PackageVersion: 2.57.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/NOISeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmphEfwHH/filef7ccd70171003/NOISeq
→ installDir: /tmp/RtmphEfwHH/filef7ccdb490f45
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on NOISeq ─────────────────────────────────────────────────
* 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 2.13.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
TissueMicroarray, ExperimentalDesign, BatchEffect, Normalization, KEGG,
PrincipalComponent, TimeCourse
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 (25%).
* 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:
    • NOISeq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • NOISeq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of NOISeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/allMD.R (line 219, column 11)
    • ...
    • R/saturation.plot.R (line 158, column 38)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • allMD.R (line 197, column 35)
    • ...
    • saturation.plot.R (line 288, column 69)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/allMD.R (line 529, column 7)
    • ...
    • print() in R/QCreport.R (line 622, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/allMD.R (line 35, column 17)
    • ...
    • R/saturation.plot.R (line 251, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/allMD.R (line 62, column 16)
    • ...
    • R/saturation.plot.R (line 15, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/auxiliar.R (line 237, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • DE.plot.R (line 7, column 21)
    • degenes.R (line 7, column 21)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/noiseqbio.R (line 54, column 30)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/NOISeq.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/fewreplicates.R (line 19, column 8)
  • suppressWarnings() in R/filter.low.counts.R (line 57, column 24)
  • suppressWarnings() in R/filter.low.counts.R (line 65, column 39)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 30
functions greater than 50 lines.
  The longest 5 functions are:
    • QCreport() (R/QCreport.R): 595 lines
    • ...
    • biodetection.plot() (R/biodetection.plot.R): 201 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/example.Rd
    • man/Marioni.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Biodetection.Rd
    • ...
    • man/Saturation.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; 1128 lines (13%) are > 80 characters long.
  First few lines:
    • R/allMD.R#L1 allMD <- function (input, factor, condit ...
    • ...
    • vignettes/NOISeq.Rnw#L1127 \newblock A scaling normalization method ...
ℹ NOTE: Consider 4 spaces instead of tabs; 190 lines (2%) contain tabs.
  First few lines:
    • R/ARSyNcomponents.R#L14 #library(Matrix) ...
    • ...
    • man/Saturation.Rd#L61 to be plotted for each selected sampl ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3091 lines (36%) are
not.
  First few lines:
    • R/allMD.R#L7 ...
    • ...
    • vignettes/NOISeq.Rnw#L1121 expression in {mRNA-Seq} experiments. ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 6 WARNINGS | ℹ 18 NOTES
ℹ See the NOISeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.