##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('IsoformSwitchAnalyzeR_2.13.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################
── Installing IsoformSwitchAnalyzeR ────────────────────────────────────────────
✔ Package installed successfully
── IsoformSwitchAnalyzeR session metadata ──────────────────────────────────────
→ sourceDir: /tmp/RtmphMSlzm/filec688b5e1d4fc1/IsoformSwitchAnalyzeR
→ BiocVersion: 3.24
→ Package: IsoformSwitchAnalyzeR
→ PackageVersion: 2.13.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/IsoformSwitchAnalyzeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmphMSlzm/filec688b5e1d4fc1/IsoformSwitchAnalyzeR
→ installDir: /tmp/RtmphMSlzm/filec688b68ba698b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on IsoformSwitchAnalyzeR ──────────────────────────────────
* 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 4.2 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/RtmphMSlzm/filec688b5e1d4fc1/IsoformSwitchAnalyzeR/man/exportToPairedGSEA.Rd'
Warning in FUN(X[[i]], ...) :
incomplete final line found on '/tmp/RtmphMSlzm/filec688b5e1d4fc1/IsoformSwitchAnalyzeR/man/importPairedGSEA.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
LongRead, Microarray, Metabolomics, Proteomics, Epigenetics, Cheminformatics,
GenomeAssembly, Normalization, Preprocessing, Bayesian, Clustering, Regression,
ExonArray, OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray,
ProprietaryPlatforms, SingleCell, CellBiology, GeneSetEnrichment,
ExperimentalDesign, QualityControl, TimeCourse
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• IsoformSwitchAnalyzeR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of IsoformSwitchAnalyzeR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
Found in files:
• R/analyze_alternative_splicing.R (line 669, column 40)
• ...
• R/tools.R (line 1915, column 40)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• analyze_alternative_splicing.R (line 143, column 37)
• ...
• tools.R (line 1989, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/analyze_alternative_splicing.R (line 1953, column 13)
• ...
• print() in R/plot_all_iso_switch.R (line 408, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/analyze_alternative_splicing.R (line 349, column 18)
• ...
• R/test_isoform_switches.R (line 1181, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/analyze_alternative_splicing.R (line 2604, column 17)
• ...
• R/tools.R (line 2241, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/analyze_alternative_splicing.R (line 823, column 24)
• ...
• R/isoform_plots.R (line 1834, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• analyze_alternative_splicing.R (line 804, column 58)
• ...
• tools.R (line 1946, column 39)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/isoformToIsoformFraction.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 69 times)
• suppressWarnings() in R/analyze_alternative_splicing.R (line 2241, column
30)
• ...
• suppressMessages() in R/tools.R (line 957, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 68
functions greater than 50 lines.
The longest 5 functions are:
• compareAnnotationOfTwoIsoforms() (R/analyze_switch_consequences.R): 2527
lines
• ...
• importCufflinksFiles() (R/import_data.R): 1137 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
• analyzeNetSurfP3.Rd
• ...
• switchPlotTopSwitches.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
Found in files:
• importCufflinksGalaxyData.Rd
ℹ NOTE: Use donttest instead of dontrun.
Found in files:
• importCufflinksGalaxyData.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; 2572 lines (8%) are > 80 characters long.
First few lines:
• R/analyze_alternative_splicing.R#L10 return( isoIndex[which( dat ...
• ...
• vignettes/IsoformSwitchAnalyzeR.Rmd#L2672 As the continued updates might
change th ...
ℹ NOTE: Consider 4 spaces instead of tabs; 32 lines (0%) contain tabs.
First few lines:
• R/analyze_alternative_splicing.R#L1160 sampleCol1 <- which(colnames ...
• ...
• R/import_data.R#L442 colnames(isoformDiffanalysis ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2100 lines (7%) are
not.
First few lines:
• R/analyze_alternative_splicing.R#L507 A5.sta ...
• ...
• vignettes/IsoformSwitchAnalyzeR.Rmd#L807 geom_point( ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 21 NOTES
ℹ See the IsoformSwitchAnalyzeR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
