##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RUVSeq_1.47.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################
── Installing RUVSeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── RUVSeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpIPWloc/file12759278228011/RUVSeq
→ BiocVersion: 3.24
→ Package: RUVSeq
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RUVSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpIPWloc/file12759278228011/RUVSeq
→ installDir: /tmp/RtmpIPWloc/file127592747e266c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RUVSeq ─────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, Proteomics, Epigenetics, Transcriptomics, Coverage, Normalization,
Pathways, Bayesian, Clustering, Regression, DNAMethylation, GeneExpression,
ChIPSeq, SingleCell, CellBiology, BiomedicalInformatics, FunctionalGenomics,
SystemsBiology, AlternativeSplicing, DifferentialMethylation,
DifferentialSplicing, GeneSetEnrichment, BatchEffect, MultipleComparison,
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 04-15-2014
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (60%).
* 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: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
Update the following files:
• RUVSeq.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• RUVSeq.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RUVSeq...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• helper.R (line 15, column 13)
• ...
• RUVs-methods.R (line 51, column 30)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
Found in files:
• RUVg-methods.R (line 30, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/RUVg-methods.R (line 7, column 25)
• R/RUVr-methods.R (line 7, column 23)
• R/RUVs-methods.R (line 7, column 23)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/makeGroups.Rd
• ...
• man/RUVs.Rd
* Checking package NEWS...
* 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; 60 lines (10%) are > 80 characters long.
First few lines:
• R/AllGenerics.R#L3 def = function(x, cIdx, k, dr ...
• ...
• vignettes/RUVSeq.Rmd#L260 First, we need to compute the residuals ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 116 lines (19%) are
not.
First few lines:
• R/AllGenerics.R#L2 name = "RUVg", ...
• ...
• vignettes/RUVSeq.Rmd#L220 design = ~ ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 10 NOTES
ℹ See the RUVSeq.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
