##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('frma_1.65.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing frma ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── frma session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUoExSy/file9ec2931cb464b/frma
→ BiocVersion: 3.24
→ Package: frma
→ PackageVersion: 1.65.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/frma.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUoExSy/file9ec2931cb464b/frma
→ installDir: /tmp/RtmpUoExSy/file9ec297e3cc5f9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on frma ───────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUoExSy/file9ec2931cb464b/frma/man/frmaExpressionSet-class.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: GeneExpression
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 (64%).
* 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:
    • frma.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • frma.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/frma.Rnw
* Checking package installation calls in R code...
* Checking for library/require of frma...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/barcode.R (line 48, column 5)
    • require() in R/frma.R (line 37, column 5)
    • require() in R/GNUSE.R (line 8, column 5)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • batchFit.R (line 17, column 60)
    • ...
    • frmaFeatureSet.R (line 104, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/barcode.R (line 48, column 61)
    • ...
    • R/GNUSE.R (line 8, column 61)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/barcode.R (line 70, column 57)
    • R/GNUSE.R (line 3, column 40)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • frma.R (line 7, column 19)
    • ...
    • frma.R (line 47, column 19)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • frmaFeatureSet() (R/frmaFeatureSet.R): 141 lines
    • ...
    • frma() (R/frma.R): 80 lines
* Checking man page documentation...
* 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; 117 lines (9%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L2 setGeneric("as.ExpressionSet", function( ...
    • ...
    • vignettes/frma.Rnw#L289 \item {\bf{lod}:} a vector of LOD scor ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 468 lines (37%) are
not.
  First few lines:
    • R/AllClasses.R#L2 representation( ...
    • ...
    • vignettes/frma.Rnw#L289 \item {\bf{lod}:} a vector of LOD scor ...
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 14 NOTES
ℹ See the frma.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.