##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('marray_1.91.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing marray ───────────────────────────────────────────────────────────
✔ Package installed successfully
── marray session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpN4R8yM/filecf7dd1c3ea097/marray
→ BiocVersion: 3.24
→ Package: marray
→ PackageVersion: 1.91.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/marray.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpN4R8yM/filecf7dd1c3ea097/marray
→ installDir: /tmp/RtmpN4R8yM/filecf7dd453c4ee7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on marray ─────────────────────────────────────────────────
* 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 2.10.0 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:
GeneExpression, Transcription, Sequencing, Metabolomics, Proteomics,
Epigenetics, Cheminformatics, Transcriptomics, Normalization, Bayesian,
Clustering, Regression, ExonArray, RNASeq, OneChannel, MicroRNAArray,
mRNAMicroarray, ProprietaryPlatforms, CellBiology, BiomedicalInformatics,
FunctionalGenomics, SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialExpression, DifferentialSplicing, GeneSetEnrichment, BatchEffect,
MultipleComparison, QualityControl, TimeCourse, DataImport
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 '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:
    • marray.Rnw
    • ...
    • marrayPlots.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • marrayClasses.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • marray.Rnw
    • ...
    • marrayPlots.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/marray.Rnw
    • ...
    • vignettes/marrayPlots.Rnw
* Checking package installation calls in R code...
* Checking for library/require of marray...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/maAnnotate.R (line 40, column 16)
    • ...
    • require() in R/maWrap.R (line 16, column 16)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/maAnnotate.R (line 173, column 21)
    • R/maInput.R (line 723, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • maAnnotate.R (line 76, column 14)
    • ...
    • maWrap.R (line 113, column 45)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/maAnnotate.R (line 194, column 3)
    • ...
    • print() in R/maWrap.R (line 124, column 6)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/maOutput.R (line 32, column 9)
    • R/maWidget.R (line 444, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/maWrap.R (line 93, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • maAnnotate.R (line 228, column 40)
    • ...
    • maInput.R (line 716, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/checkTargetInfo.Rd
ℹ Found @ in vignettes/marray.Rnw
ℹ Found @ in vignettes/marrayClasses.Rnw
ℹ Found @ in vignettes/marrayClassesShort.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 4 times)
  • <<- in R/maWidget.R (line 118, column 41)
  • ...
  • <<- in R/maWidget.R (line 428, column 18)
* 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:
    • widget.marrayRaw() (R/maWidget.R): 250 lines
    • ...
    • read.Agilent() (R/maInput.R): 100 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/boxplot.Rd
    • ...
    • man/write.xls.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • cbind.Rd
    • ...
    • maTwoSamples.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...
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; 661 lines (6%) are > 80 characters long.
  First few lines:
    • R/maAnnotate.R#L12 mapGeneInfo <- function(widget=FALSE, Gn ...
    • ...
    • vignettes/marrayPlots.Rnw#L533 \section{Wrapper functions for basic set
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 231 lines (2%) contain tabs.
  First few lines:
    • R/maClasses.R#L15 maInfo="data.frame", ...
    • ...
    • vignettes/marrayPlots.Rnw#L483 main="Swirl array 93: post--norm ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2736 lines (25%) are
not.
  First few lines:
    • R/maAnnotate.R#L13 { ...
    • ...
    • vignettes/marrayPlots.Rnw#L518 columns. } ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the marray.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.