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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RBM_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RBM ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── RBM session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpICrZ9j/file10831d38a523a4/RBM
→ BiocVersion: 3.24
→ Package: RBM
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RBM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpICrZ9j/file10831d38a523a4/RBM
→ installDir: /tmp/RtmpICrZ9j/file10831d11bb7e02
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RBM ────────────────────────────────────────────────────
* 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 3.2.0 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/RtmpICrZ9j/file10831d38a523a4/RBM/man/ovarian_cancer_methylation.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, Metabolomics, Proteomics, Epigenetics, Cheminformatics,
Transcriptomics, Normalization, Preprocessing, Bayesian, Clustering,
Regression, ExonArray, GeneExpression, RNASeq, OneChannel, TwoChannel,
MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialSplicing, GeneSetEnrichment, BatchEffect,
MultipleComparison, QualityControl, TimeCourse, 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 (100%).
* 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:
• RBM.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• RBM.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/RBM.Rnw
* Checking package installation calls in R code...
* Checking for library/require of RBM...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• RBM_package.R (line 16, column 15)
• ...
• RBM_package.R (line 135, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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...
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; 50 lines (9%) are > 80 characters long.
First few lines:
• R/RBM_package.R#L40 permutation_p = permu ...
• ...
• vignettes/RBM.Rnw#L193 sig_results_boot <- cbind(ovarian_cancer ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 105 lines (19%) are
not.
First few lines:
• R/RBM_package.R#L2 function (aData, vec_trt, repetition, ...
• ...
• vignettes/RBM.Rnw#L153 ...
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 Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 12 NOTES
ℹ See the RBM.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
