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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('IWTomics_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing IWTomics ─────────────────────────────────────────────────────────
✔ Package installed successfully
── IWTomics session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics
→ BiocVersion: 3.24
→ Package: IWTomics
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/IWTomics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics
→ installDir: /tmp/RtmpTzN7dM/filec6e314c1dc495
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on IWTomics ───────────────────────────────────────────────
* 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 3.5.0 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/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/IWTomics-package.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/IWTomicsData-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/IWTomicsTest.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/plot-IWTomicsData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/plotSummary.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/plotTest.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/regions_example.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpTzN7dM/filec6e316a92a0ec/IWTomics/man/smooth-IWTomicsData.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, Alignment
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 (21%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • IWTomics.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • IWTomics.Rnw
* Checking package installation calls in R code...
* Checking for library/require of IWTomics...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotSummary.R (line 424, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • IWTomicsData-class.R (line 187, column 28)
    • ...
    • plotTest.R (line 140, column 50)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/IWTomicsData-class.R (line 35, column 28)
    • ...
    • R/smooth-IWTomicsData.R (line 341, column 8)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/IWTomicsData-class.R (line 117, column 25)
    • R/IWTomicsData-class.R (line 120, column 22)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • IWTomicsTest.R (line 5, column 28)
    • plotSummary.R (line 7, column 28)
    • plotTest.R (line 7, column 28)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/IWTomicsTest.R (line 107, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.3() (R/smooth-IWTomicsData.R): 323 lines
    • ...
    • .IWTomics.2pop() (R/IWTomicsTest.R): 183 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • IWTomics-internal.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; 1001 lines (21%) are > 80 characters long.
  First few lines:
    • R/IWTomicsData-class.R#L17 if(!(alignment(objec ...
    • ...
    • vignettes/IWTomics.Rnw#L626 Figure \ref{relevant_scale} indicates th ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (0%) contain tabs.
  First few lines:
    • IWTomics/NAMESPACE#L17 nRegions,nFeatures,lengthRegions,length ...
    • ...
    • vignettes/IWTomics.Rnw#L148 chr2 49962150 49964150 0.781642204257823 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2026 lines (43%) are
not.
  First few lines:
    • R/IWTomicsData-class.R#L3 slots=c(metadata="list", ...
    • ...
    • vignettes/IWTomics.Rnw#L622 id_features_su ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the IWTomics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.