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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ASpli_2.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ASpli ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ASpli session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplHK5B9/file5716947fe3361/ASpli
→ BiocVersion: 3.24
→ Package: ASpli
→ PackageVersion: 2.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ASpli.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplHK5B9/file5716947fe3361/ASpli
→ installDir: /tmp/RtmplHK5B9/file571696dcbea87
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ASpli ──────────────────────────────────────────────────
* 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/RtmplHK5B9/file5716947fe3361/ASpli/man/ASpliAS-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmplHK5B9/file5716947fe3361/ASpli/man/ASpliIntegratedSignals-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmplHK5B9/file5716947fe3361/ASpli/man/ASpliJDU-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmplHK5B9/file5716947fe3361/ASpli/man/ASpliSplicingReport-class.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
Metabolomics, Proteomics, Epigenetics, Cheminformatics, Transcriptomics,
Normalization, Pathways, Preprocessing, Bayesian, Clustering, Regression,
DNAMethylation, ExonArray, ChIPSeq, OneChannel, TwoChannel, MicroRNAArray,
mRNAMicroarray, ProprietaryPlatforms, SingleCell, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology,
DifferentialMethylation, GeneSetEnrichment, BatchEffect, MultipleComparison,
QualityControl, 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (46%).
* 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:
    • ASpli.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 44 out of 53 code chunks = 83% unevaluated
ℹ 
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • ASpli.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ASpli.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ASpli.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ASpli...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ASpli_methods.R (line 1500, column 37)
    • ...
    • R/readCounts_functions.R (line 12, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ASDiscover_functions.R (line 33, column 14)
    • ...
    • splicingReport_functions.R (line 821, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/binGenome_functions.R (line 645, column 5)
    • print() in R/plotBins_functions.R (line 8, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ASDiscover_functions.R (line 133, column 8)
    • ...
    • R/subset_methods.R (line 41, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ASpli_methods.R (line 372, column 17)
    • ...
    • R/plotGenomeRegions_functions.R (line 490, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 13 times:
    • T in R/ASpli_methods.R (line 488, column 118)
    • ...
    • T in R/splicingReport_functions.R (line 51, column 68)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ASpli_methods.R (line 1453, column 36)
    • ...
    • splicingReport_functions.R (line 780, column 28)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/ASpli_methods.R (line 380, column 17)
    • ...
    • system() in R/plotBins_functions.R (line 1910, column 11)
! WARNING: .Deprecated / .Defunct usage (found 9 times)
  • .Deprecated() in R/ASpli_methods.R (line 327, column 7)
  • ...
  • .Deprecated() in R/loadBam_function.R (line 3, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/gbDUreport-method.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/common_functions.R (line 56, column 15)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 10 times)
  • suppressWarnings() in R/ASpli_methods.R (line 1591, column 9)
  • ...
  • suppressWarnings() in R/splicingReport_functions.R (line 587, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 36
functions greater than 50 lines.
  The longest 5 functions are:
    • .integrateSignals() (R/splicingReport_functions.R): 624 lines
    • ...
    • .junctionDUreportExt() (R/jDUreport_functions.R): 497 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ASpli-deprecated.Rd
    • ...
    • man/write-methods.Rd
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • acc_AS.Rd
    • ...
    • write.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; 1312 lines (8%) are > 80 characters long.
  First few lines:
    • R/ASDiscover_functions.R#L34 byCond <- cropped[ , targets$conditi ...
    • ...
    • vignettes/ASpli.Rnw#L1333 \item [NonUniformity:] if non uniform ...
ℹ NOTE: Consider 4 spaces instead of tabs; 14 lines (0%) contain tabs.
  First few lines:
    • R/ASpli_methods.R#L1501 b[, columnas_numericas] <- apply( ...
    • ...
    • vignettes/ASpli.Rnw#L827 \item sr: An object of class ASpliSplici ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 7695 lines (49%) are
not.
  First few lines:
    • R/ASDiscover_functions.R#L7 # Simple function to compute the minim ...
    • ...
    • vignettes/ASpli.Rnw#L1364 \item [J counts:] junctions' counts f ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 6 WARNINGS | ℹ 20 NOTES
ℹ See the ASpli.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.