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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RTCA_1.65.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RTCA ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── RTCA session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUXCh95/file1269d91bde076e/RTCA
→ BiocVersion: 3.24
→ Package: RTCA
→ PackageVersion: 1.65.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RTCA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUXCh95/file1269d91bde076e/RTCA
→ installDir: /tmp/RtmpUXCh95/file1269d97426243a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RTCA ───────────────────────────────────────────────────
* 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...
* 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/RtmpUXCh95/file1269d91bde076e/RTCA/man/sliceRTCA.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpUXCh95/file1269d91bde076e/RTCA/man/smoothTransform.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: 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 (17%).
* 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:
    • aboutRTCA.Rnw
    • RTCAtransformation.Rnw
* Checking package installation calls in R code...
* Checking for library/require of RTCA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/algorithms.R (line 142, column 34)
    • ...
    • R/visualization.R (line 440, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • algorithms.R (line 21, column 12)
    • ...
    • visualization.R (line 479, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/spectramaxImport.R (line 3, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/RTCAfunctions.R (line 112, column 60)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • T in R/visualization.R (line 368, column 82)
    • T in R/visualization.R (line 368, column 101)
    • T in R/visualization.R (line 412, column 42)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllClasses.R (line 17, column 34)
    • ...
    • visualization.R (line 159, column 20)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • myheatmap.2() (R/visualization.R): 333 lines
    • parseRTCA() (R/RTCAfunctions.R): 65 lines
    • controlView() (R/visualization.R): 60 lines
* Checking man page documentation...
* 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; 129 lines (5%) are > 80 characters long.
  First few lines:
    • R/algorithms.R#L57 interpolationTransform <- function(objec ...
    • ...
    • vignettes/RTCAtransformation.Rnw#L101 visualization, the smooth
    transformation ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (0%) contain tabs.
  First few lines:
    • man/RTCA-class.Rd#L69 action = "character")}: add action at t ...
    • ...
    • vignettes/RTCAtransformation.Rnw#L7 \usepackage{mathptmx} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 824 lines (31%) are
not.
  First few lines:
    • R/algorithms.R#L18 istime <- nearestTimeIndex(object, tim ...
    • ...
    • vignettes/RTCAtransformation.Rnw#L117 transformation}, as its name
    suggests, ...
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 13 NOTES
ℹ See the RTCA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.