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BiocCheckGitClone('methodical')
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─ BiocCheckVersion: 1.39.10
─ BiocVersion: 3.19
─ Package: methodical
─ PackageVersion: 0.99.17
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3169/fa49d97f3ac334c9a625fa921dd2b0879b64c619/methodical
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3169/fa49d97f3ac334c9a625fa921dd2b0879b64c619/methodical.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘0.99.17’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘methodical’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘HDF5Array:::.serialize_HDF5SummarizedExperiment’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.chunk_regions’ ‘.tss_iterator’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [29s/29s] NOTE
.calculate_regions_intersections: no visible global function definition
for ‘is’
.chunk_regions: no visible global function definition for ‘is’
.chunk_regions: no visible global function definition for
‘subsetByOverlaps’
.count_covered_bases: no visible global function definition for ‘is’
.create_meth_rse_from_hdf5: no visible global function definition for
‘setNames’
.split_bedgraph: no visible binding for global variable
‘meth_site_groups’
.split_bedgraph: no visible binding for global variable ‘total_files’
.split_bedgraph: no visible binding for global variable ‘meth_sites_df’
.split_bedgraph: no visible global function definition for ‘setNames’
.split_bedgraph: no visible binding for global variable
‘seqnames_column’
.split_bedgraph: no visible binding for global variable ‘start_column’
.split_bedgraph: no visible binding for global variable ‘end_column’
.split_bedgraph: no visible binding for global variable ‘value_column’
.split_bedgraph: no visible binding for global variable ‘dt_threads’
.split_bedgraph: no visible binding for global variable ‘zero_based’
.split_bedgraph: no visible binding for global variable
‘normalization_factor’
.split_bedgraph: no visible binding for global variable
‘decimal_places’
.split_bedgraph: no visible binding for global variable ‘mg’
.split_bedgraph: no visible binding for global variable
‘temp_chunk_dirs’
.split_meth_array_file: no visible binding for global variable
‘probe_groups’
.split_meth_array_file: no visible binding for global variable
‘total_files’
.split_meth_array_file: no visible binding for global variable
‘probe_sites_df’
.split_meth_array_file: no visible global function definition for
‘setNames’
.split_meth_array_file: no visible binding for global variable
‘probe_name_column’
.split_meth_array_file: no visible binding for global variable
‘beta_value_column’
.split_meth_array_file: no visible binding for global variable
‘normalization_factor’
.split_meth_array_file: no visible binding for global variable
‘decimal_places’
.split_meth_array_file: no visible binding for global variable ‘name’
.split_meth_array_file: no visible binding for global variable ‘pg’
.split_meth_array_file: no visible binding for global variable
‘temp_chunk_dirs’
.split_meth_array_file: no visible binding for global variable
‘dt_threads’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘name’
.summarize_chunk_methylation: no visible global function definition for
‘subsetByOverlaps’
.tss_correlations: no visible global function definition for ‘setNames’
.write_chunks_to_hdf5: no visible binding for global variable ‘chunk’
annotateGRanges: no visible global function definition for ‘is’
annotatePlot: no visible global function definition for ‘is’
annotatePlot: no visible global function definition for
‘colorRampPalette’
annotatePlot: no visible global function definition for
‘subsetByOverlaps’
annotatePlot: no visible binding for global variable ‘region_type’
calculateMethSiteTranscriptCors: no visible global function definition
for ‘is’
calculateMethSiteTranscriptCors: no visible binding for global variable
‘chunk’
calculateMethSiteTranscriptCors: no visible global function definition
for ‘subsetByOverlaps’
calculateMethSiteTranscriptCors: no visible global function definition
for ‘setNames’
calculateRegionMethylationTranscriptCors: no visible global function
definition for ‘is’
calculateRegionMethylationTranscriptCors: no visible binding for global
variable ‘p.adjust.methods’
calculateRegionMethylationTranscriptCors : <anonymous>: no visible
global function definition for ‘setNames’
calculateRegionMethylationTranscriptCors: no visible global function
definition for ‘p.adjust’
calculateSmoothedMethodicalScores: no visible global function
definition for ‘is’
createRandomRegions: no visible global function definition for ‘is’
createRandomRegions: no visible global function definition for
‘seqlengths’
createRandomRegions: no visible global function definition for
‘overlapsAny’
extractGRangesMethSiteValues: no visible global function definition for
‘is’
extractMethSitesFromGenome: no visible global function definition for
‘is’
findTMRs: no visible global function definition for ‘is’
kallistoIndex: no visible global function definition for ‘is’
kallistoQuantify: no visible global function definition for ‘is’
kallistoQuantify: no visible global function definition for ‘setNames’
liftoverMethRSE: no visible global function definition for ‘is’
makeMethRSEFromArrayFiles: no visible global function definition for
‘is’
makeMethRSEFromBedgraphs: no visible global function definition for
‘is’
maskRangesInRSE: no visible global function definition for ‘is’
maskRangesInRSE: no visible global function definition for ‘queryHits’
methrixToRSE: no visible global function definition for ‘is’
plotMethSiteCorCoefs: no visible global function definition for ‘is’
plotMethSiteCorCoefs: no visible binding for global variable ‘cor’
plotMethSiteCorCoefs: no visible global function definition for
‘complete.cases’
plotMethSiteCorCoefs: no visible binding for global variable
‘meth_cor_plot_position’
plotMethodicalScores: no visible global function definition for ‘is’
plotMethodicalScores: no visible global function definition for
‘seqlevels’
plotMethodicalScores: no visible binding for global variable
‘meth_site_start’
plotMethodicalScores: no visible binding for global variable
‘meth_site_plot_position’
plotMethodicalScores: no visible binding for global variable
‘methodical_score’
plotMethodicalScores: no visible binding for global variable ‘cor’
plotMethylationValues: no visible global function definition for ‘is’
plotMethylationValues: no visible global function definition for
‘complete.cases’
plotMethylationValues: no visible binding for global variable
‘meth_site_plot_position’
plotTMRs: no visible global function definition for ‘is’
plotTMRs: no visible binding for global variable ‘direction’
plotTMRs: no visible global function definition for ‘setNames’
rangesRelativeToTSS: no visible global function definition for ‘is’
rapidCorTest: no visible global function definition for ‘is’
rapidCorTest: no visible binding for global variable ‘p.adjust.methods’
rapidCorTest: no visible global function definition for ‘cor’
rapidCorTest: no visible global function definition for ‘pt’
rapidCorTest: no visible global function definition for ‘p.adjust’
sampleMethSites: no visible global function definition for ‘is’
strandedDistance: no visible global function definition for ‘is’
sumTranscriptValuesForGenes: no visible global function definition for
‘is’
sumTranscriptValuesForGenes : <anonymous>: no visible global function
definition for ‘is’
sumTranscriptValuesForGenes: no visible binding for global variable
‘gene_transcripts’
summarizeRegionMethylation: no visible global function definition for
‘is’
summarizeRegionMethylation: no visible global function definition for
‘seqlevels’
Undefined global functions or variables:
beta_value_column chunk colorRampPalette complete.cases cor
decimal_places direction dt_threads end_column gene_transcripts is
meth_cor_plot_position meth_site_groups meth_site_plot_position
meth_site_start meth_sites_df methodical_score mg name
normalization_factor overlapsAny p.adjust p.adjust.methods pg
probe_groups probe_name_column probe_sites_df pt queryHits
region_type seqlengths seqlevels seqnames_column setNames
start_column subsetByOverlaps temp_chunk_dirs total_files
value_column zero_based
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("methods", "is")
importFrom("stats", "complete.cases", "cor", "p.adjust",
"p.adjust.methods", "pt", "setNames")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to attach():
File ‘methodical/R/make_meth_rse_accessory_functions.R’:
attach(parameters)
attach(parameters)
See section ‘Good practice’ in ‘?attach’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'annotateGRanges.Rd':
\examples lines wider than 100 characters:
repeat_annotation_hg38 <- GRangesList(split(repeat_annotation_hg38, repeat_annotation_hg38$repClass))
# Calculate the proportion of base pairs in CpG islands overlapping different classes of repetitive elements
annotateGRanges(genomic_regions = cpg_island_annotation, annotation_ranges = repeat_annotation_hg38, overlap_measure = "proportion")
Rd file 'annotatePlot.Rd':
\examples lines wider than 100 characters:
methodical::annotatePlot(tubb6_correlation_plot, annotation_grl = cpg_island_annotation, annotation_plot_proportion = 0.3)
Rd file 'calculateMethSiteTranscriptCors.Rd':
\examples lines wider than 100 characters:
# Load TUBB6 TSS GRanges, RangedSummarizedExperiment with methylation values for CpGs around TUBB6 TSS and TUBB6 transcript counts
tubb6_cpg_meth_transcript_cors <- methodical::calculateMethSiteTranscriptCors(meth_rse = tubb6_meth_rse,
transcript_expression_table = tubb6_transcript_counts, tss_gr = tubb6_tss, expand_upstream = 5000, expand_downstream = 5000)
Rd file 'calculateRegionMethylationTranscriptCors.Rd':
\examples lines wider than 100 characters:
# Load TUBB6 TMRs, RangedSummarizedExperiment with methylation values for CpGs around TUBB6 TSS and TUBB6 transcript counts
Rd file 'calculateSmoothedMethodicalScores.Rd':
\examples lines wider than 100 characters:
smoothed_methodical_scores <- methodical::calculateSmoothedMethodicalScores(tubb6_cpg_meth_transcript_cors)
Rd file 'createRandomRegions.Rd':
\examples lines wider than 100 characters:
random_regions <- methodical::createRandomRegions(genome = "BSgenome.Hsapiens.UCSC.hg38", n_regions = 10000)
Rd file 'extractGRangesMethSiteValues.Rd':
\examples lines wider than 100 characters:
test_region_methylation <- methodical::extractGRangesMethSiteValues(meth_rse = tubb6_meth_rse, genomic_regions = test_region)
Rd file 'extractMethSitesFromGenome.Rd':
\examples lines wider than 100 characters:
arabidopsis_cphpgs <- methodical::extractMethSitesFromGenome("BSgenome.Athaliana.TAIR.TAIR9", pattern = "CHG")
Rd file 'kallistoIndex.Rd':
\examples lines wider than 100 characters:
download.file("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz")
Rd file 'liftoverMethRSE.Rd':
\examples lines wider than 100 characters:
# Liftover tubb6_meth_rse from hg38 to hg19, keeping only sites that were mapped to CpG sites in hg19
Rd file 'plotMethSiteCorCoefs.Rd':
\examples lines wider than 100 characters:
ylabel = "Spearman Correlation", reference_tss = attributes(tubb6_cpg_meth_transcript_cors)$tss_range)
Rd file 'plotMethodicalScores.Rd':
\examples lines wider than 100 characters:
methodical::plotMethodicalScores(tubb6_cpg_meth_transcript_cors, reference_tss = attributes(tubb6_cpg_meth_transcript_cors)$tss_range)
Rd file 'plotTMRs.Rd':
\examples lines wider than 100 characters:
tubb6_correlation_plot <- methodical::plotMethSiteCorCoefs(tubb6_cpg_meth_transcript_cors, ylabel = "Spearman Correlation")
Rd file 'sampleMethSites.Rd':
\examples lines wider than 100 characters:
random_cpgs <- methodical::sampleMethSites(tubb6_meth_rse, n_sites = 20, genomic_ranges_filter = mask_ranges,
Rd file 'summarizeRegionMethylation.Rd':
\examples lines wider than 100 characters:
test_gr <- GRanges(c("chr18:12303400-12303500", "chr18:12303600-12303750", "chr18:12304000-12306000"))
test_gr_methylation <- methodical::summarizeRegionMethylation(tubb6_meth_rse, genomic_regions = test_gr,
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [10s/10s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [358s/358s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
extractMethSitesFromGenome 124.554 14.080 139.402
liftoverMethRSE 102.892 10.545 114.824
annotateGRanges 28.433 3.730 34.352
makeMethRSEFromArrayFiles 8.349 2.758 8.884
makeMethRSEFromBedgraphs 5.951 1.899 5.251
calculateMethSiteTranscriptCors 6.824 0.911 7.680
summarizeRegionMethylation 4.834 1.052 5.783
calculateRegionMethylationTranscriptCors 4.647 1.133 5.770
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3169/fa49d97f3ac334c9a625fa921dd2b0879b64c619/methodical.Rcheck/00check.log’
for details.
===============================
BiocCheck('methodical_0.99.17.tar.gz')
===============================
─ BiocCheckVersion: 1.39.10
─ BiocVersion: 3.19
─ Package: methodical
─ PackageVersion: 0.99.17
─ sourceDir: /tmp/RtmphnFztX/file2e834553c7ca57/methodical
─ installDir: /tmp/RtmphnFztX/file2e834575198ffb
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3169/fa49d97f3ac334c9a625fa921dd2b0879b64c619/methodical.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.3.0 to 4.4.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Sequencing, Coverage
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of methodical...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 1 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 18 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 2% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* 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...
* NOTE: Consider shorter lines; 954 lines (23%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1660 lines
(40%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 15 NOTES
See the methodical.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.