nebbiolo2 Summary
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| Package: methodical |
| Version: 0.99.6 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data methodical |
| BuildTime: 0 minutes 52.80 seconds |
| CheckCommand: BiocCheckGitClone('methodical') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3169/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/methodical.install-out.txt methodical_0.99.6.tar.gz && BiocCheck('methodical_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 8 minutes 3.03 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 4398.13 KiB |
| BuildID:: methodical_20231018103502 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: methodical. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘methodical/DESCRIPTION’ ... OK
* preparing ‘methodical’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘methodical_0.99.6.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('methodical')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/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/eb3920a8b574701dd57430efb442c72e4277035a/methodical.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* 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 ‘0.99.6’
* 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 ... OK
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [22s/22s] NOTE
.chunk_regions: no visible global function definition for
‘subsetByOverlaps’
.create_meth_rse_from_hdf5: no visible global function definition for
‘setNames’
.split_bedgraphs_into_chunks: no visible global function definition for
‘%dopar%’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘column’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘file_count’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘bg_file’
.split_bedgraphs_into_chunks: no visible global function definition for
‘setNames’
.split_bedgraphs_into_chunks: no visible global function definition for
‘%do%’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘mg’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘name’
.split_meth_array_files_into_chunks: no visible global function
definition for ‘%dopar%’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘column’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘file_count’
.split_meth_array_files_into_chunks: no visible global function
definition for ‘setNames’
.split_meth_array_files_into_chunks: no visible global function
definition for ‘%do%’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘pg’
.write_chunks_to_hdf5: no visible binding for global variable ‘chunk’
annotate_granges: no visible global function definition for ‘is’
annotate_meth_site_plot: no visible global function definition for
‘subsetByOverlaps’
annotate_meth_site_plot: no visible global function definition for
‘setNames’
annotate_meth_site_plot: no visible global function definition for
‘colorRampPalette’
annotate_meth_site_plot: no visible binding for global variable
‘region_type’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘%do%’
calculate_meth_site_transcript_cors: no visible binding for global
variable ‘chunk’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘subsetByOverlaps’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘%dopar%’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘setNames’
calculate_meth_site_transcript_cors: no visible binding for global
variable ‘transcript_name’
calculate_meth_site_transcript_cors: no visible binding for global
variable ‘transcript_tss’
calculate_region_methylation_transcript_cors: no visible binding for
global variable ‘transcript’
calculate_region_methylation_transcript_cors: no visible global
function definition for ‘setNames’
calculate_region_methylation_transcript_cors: no visible global
function definition for ‘p.adjust’
create_random_regions: no visible global function definition for
‘seqlengths’
create_random_regions: no visible global function definition for
‘overlapsAny’
download_meth_dataset: no visible global function definition for ‘data’
download_meth_dataset: no visible binding for global variable
‘TumourMethDatasets’
expand_granges: no visible global function definition for ‘is’
expand_granges: no visible global function definition for ‘IRanges’
kallisto_quantify: no visible global function definition for ‘setNames’
mask_ranges_in_rse: no visible global function definition for ‘is’
mask_ranges_in_rse: no visible global function definition for
‘queryHits’
plot_meth_site_values: no visible global function definition for ‘is’
plot_meth_site_values: no visible global function definition for
‘complete.cases’
plot_meth_site_values: no visible binding for global variable
‘meth_site_plot_position’
plot_methodical_scores: no visible global function definition for
‘seqlevels’
plot_methodical_scores: no visible binding for global variable
‘meth_site_start’
plot_methodical_scores: no visible binding for global variable
‘meth_site_plot_position’
plot_methodical_scores: no visible binding for global variable
‘methodical_score’
plot_methodical_scores: no visible binding for global variable ‘cor’
plot_tmrs: no visible binding for global variable ‘direction’
plot_tmrs: no visible global function definition for ‘setNames’
rapid_cor_test: no visible global function definition for ‘cor’
rapid_cor_test: no visible global function definition for ‘pt’
rapid_cor_test: no visible global function definition for ‘p.adjust’
sum_transcript_values_for_genes: no visible global function definition
for ‘is’
sum_transcript_values_for_genes: no visible binding for global variable
‘gene_transcripts’
summarize_region_methylation: no visible global function definition for
‘is’
summarize_region_methylation: no visible global function definition for
‘seqlevels’
summarize_region_methylation: no visible global function definition for
‘%dopar%’
summarize_region_methylation: no visible binding for global variable
‘chunk’
summarize_region_methylation: no visible global function definition for
‘subsetByOverlaps’
Undefined global functions or variables:
%do% %dopar% IRanges TumourMethDatasets bg_file chunk
colorRampPalette column complete.cases cor data direction file_count
gene_transcripts is meth_site_plot_position meth_site_start
methodical_score mg name overlapsAny p.adjust pg pt queryHits
region_type seqlengths seqlevels setNames subsetByOverlaps transcript
transcript_name transcript_tss
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("methods", "is")
importFrom("stats", "complete.cases", "cor", "p.adjust", "pt",
"setNames")
importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to data() loading into the global environment:
File ‘methodical/R/download_datasets.R’:
data("TumourMethDatasets", package = "methodical")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'annotate_meth_site_plot.Rd':
\examples lines wider than 100 characters:
methodical::annotate_meth_site_plot(tubb6_correlation_plot, cpg_island_annotation, annotation_plot_height = 0.3)
Rd file 'calculate_meth_site_transcript_cors.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::calculate_meth_site_transcript_cors(meth_rse = tubb6_meth_rse,
transcript_expression_table = tubb6_transcript_counts, tss_gr = tubb6_tss, expand_upstream = 5000, expand_downstream = 5000)
Rd file 'calculate_region_methylation_transcript_cors.Rd':
\examples lines wider than 100 characters:
# Load TUBB6 TMRs, RangedSummarizedExperiment with methylation values for CpGs around TUBB6 TSS and TUBB6 transcript counts
genomic_regions = tubb6_tmrs, genomic_region_names = tubb6_tmrs$tmr_name, meth_rse = tubb6_meth_rse, transcript_expression_table = tu ... [TRUNCATED]
Rd file 'calculate_smoothed_methodical_scores.Rd':
\examples lines wider than 100 characters:
smoothed_methodical_scores = methodical::calculate_smoothed_methodical_scores(tubb6_cpg_meth_transcript_cors)
Rd file 'create_random_regions.Rd':
\examples lines wider than 100 characters:
random_regions = methodical::create_random_regions(genome = "BSgenome.Hsapiens.UCSC.hg38", n_regions = 10000)
Rd file 'extract_granges_meth_site_values.Rd':
\examples lines wider than 100 characters:
test_region_methylation = methodical::extract_granges_meth_site_values(tubb6_meth_rse, genomic_regions = test_region)
Rd file 'extract_meth_sites_from_genome.Rd':
\examples lines wider than 100 characters:
arabidopsis_cphpgs = methodical::extract_meth_sites_from_genome("BSgenome.Athaliana.TAIR.TAIR9", pattern = "CHG")
Rd file 'kallisto_index.Rd':
\examples lines wider than 100 characters:
download.file("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz")
Rd file 'liftover_meth_rse.Rd':
\examples lines wider than 100 characters:
# Liftover tubb6_meth_rse from hg38 to hg19, keeping only sites that were mapped to CpG sites in hg19
Rd file 'plot_meth_site_values.Rd':
\examples lines wider than 100 characters:
methodical::plot_meth_site_values(tubb6_cpg_meth_transcript_cors, column_name = "cor", ylabel = "Spearman Correlation")
ylabel = "Spearman Correlation", reference_tss = attributes(tubb6_cpg_meth_transcript_cors)$tss_range)
Rd file 'plot_methodical_scores.Rd':
\examples lines wider than 100 characters:
methodical::plot_methodical_scores(tubb6_cpg_meth_transcript_cors, reference_tss = attributes(tubb6_cpg_meth_transcript_cors)$tss_range ... [TRUNCATED]
Rd file 'plot_tmrs.Rd':
\examples lines wider than 100 characters:
tubb6_correlation_plot = methodical::plot_meth_site_values(tubb6_cpg_meth_transcript_cors, column_name = "cor", ylabel = "Spearman Corr ... [TRUNCATED]
Rd file 'sample_meth_sites.Rd':
\examples lines wider than 100 characters:
random_cpgs = methodical::sample_meth_sites(tubb6_meth_rse, n_sites = 20, genomic_ranges_filter = mask_ranges,
Rd file 'summarize_region_methylation.Rd':
\examples lines wider than 100 characters:
test_gr = GRanges(c("chr18:12303400-12303500", "chr18:12303600-12303750", "chr18:12304000-12306000"))
test_gr_methylation = methodical::summarize_region_methylation(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 ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [319s/320s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
extract_meth_sites_from_genome 124.114 11.524 135.649
liftover_meth_rse 100.222 10.118 111.005
make_meth_rse_from_array_files 10.667 0.090 8.223
annotate_meth_site_plot 7.555 0.478 8.607
make_meth_rse_from_bedgraphs 6.529 0.018 5.988
download_meth_dataset 4.176 0.160 6.919
* 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/methodical.Rcheck/00check.log’
for details.
===============================
BiocCheck('methodical_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmplrvrXJ/file264fe034ecf3fd/methodical
─ installDir: /tmp/RtmplrvrXJ/file264fe073766a2d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/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 4.0 to 4.3.0.
* 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, GenomeWideAssociation
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...
* NOTE: Provide 'URL' field(s) 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...
* WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 15 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; 1121 lines (22%) are > 80
characters long.
* NOTE: Consider multiples of 4 spaces for line indents; 1663 lines
(32%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 17 NOTES
See the methodical.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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lconway Summary
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| Package: methodical |
| Version: 0.99.6 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data methodical |
| BuildTime: 0 minutes 37.79 seconds |
| CheckCommand: BiocCheckGitClone('methodical') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3169/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/methodical.install-out.txt methodical_0.99.6.tar.gz && BiocCheck('methodical_0.99.6.tar.gz', `new-package`=TRUE) |
| CheckTime: 6 minutes 20.61 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh methodical_0.99.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 15.74 seconds |
| PackageFileSize: 4398.06 KiB |
| BuildID:: methodical_20231018103502 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: methodical. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘methodical/DESCRIPTION’ ... OK
* preparing ‘methodical’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘methodical_0.99.6.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('methodical')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/methodical.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘0.99.6’
* 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 ... OK
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
.chunk_regions: no visible global function definition for
‘subsetByOverlaps’
.create_meth_rse_from_hdf5: no visible global function definition for
‘setNames’
.split_bedgraphs_into_chunks: no visible global function definition for
‘%dopar%’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘column’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘file_count’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘bg_file’
.split_bedgraphs_into_chunks: no visible global function definition for
‘setNames’
.split_bedgraphs_into_chunks: no visible global function definition for
‘%do%’
.split_bedgraphs_into_chunks: no visible binding for global variable
‘mg’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘name’
.split_meth_array_files_into_chunks: no visible global function
definition for ‘%dopar%’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘column’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘file_count’
.split_meth_array_files_into_chunks: no visible global function
definition for ‘setNames’
.split_meth_array_files_into_chunks: no visible global function
definition for ‘%do%’
.split_meth_array_files_into_chunks: no visible binding for global
variable ‘pg’
.write_chunks_to_hdf5: no visible binding for global variable ‘chunk’
annotate_granges: no visible global function definition for ‘is’
annotate_meth_site_plot: no visible global function definition for
‘subsetByOverlaps’
annotate_meth_site_plot: no visible global function definition for
‘setNames’
annotate_meth_site_plot: no visible global function definition for
‘colorRampPalette’
annotate_meth_site_plot: no visible binding for global variable
‘region_type’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘%do%’
calculate_meth_site_transcript_cors: no visible binding for global
variable ‘chunk’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘subsetByOverlaps’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘%dopar%’
calculate_meth_site_transcript_cors: no visible global function
definition for ‘setNames’
calculate_meth_site_transcript_cors: no visible binding for global
variable ‘transcript_name’
calculate_meth_site_transcript_cors: no visible binding for global
variable ‘transcript_tss’
calculate_region_methylation_transcript_cors: no visible binding for
global variable ‘transcript’
calculate_region_methylation_transcript_cors: no visible global
function definition for ‘setNames’
calculate_region_methylation_transcript_cors: no visible global
function definition for ‘p.adjust’
create_random_regions: no visible global function definition for
‘seqlengths’
create_random_regions: no visible global function definition for
‘overlapsAny’
download_meth_dataset: no visible global function definition for ‘data’
download_meth_dataset: no visible binding for global variable
‘TumourMethDatasets’
expand_granges: no visible global function definition for ‘is’
expand_granges: no visible global function definition for ‘IRanges’
kallisto_quantify: no visible global function definition for ‘setNames’
mask_ranges_in_rse: no visible global function definition for ‘is’
mask_ranges_in_rse: no visible global function definition for
‘queryHits’
plot_meth_site_values: no visible global function definition for ‘is’
plot_meth_site_values: no visible global function definition for
‘complete.cases’
plot_meth_site_values: no visible binding for global variable
‘meth_site_plot_position’
plot_methodical_scores: no visible global function definition for
‘seqlevels’
plot_methodical_scores: no visible binding for global variable
‘meth_site_start’
plot_methodical_scores: no visible binding for global variable
‘meth_site_plot_position’
plot_methodical_scores: no visible binding for global variable
‘methodical_score’
plot_methodical_scores: no visible binding for global variable ‘cor’
plot_tmrs: no visible binding for global variable ‘direction’
plot_tmrs: no visible global function definition for ‘setNames’
rapid_cor_test: no visible global function definition for ‘cor’
rapid_cor_test: no visible global function definition for ‘pt’
rapid_cor_test: no visible global function definition for ‘p.adjust’
sum_transcript_values_for_genes: no visible global function definition
for ‘is’
sum_transcript_values_for_genes: no visible binding for global variable
‘gene_transcripts’
summarize_region_methylation: no visible global function definition for
‘is’
summarize_region_methylation: no visible global function definition for
‘seqlevels’
summarize_region_methylation: no visible global function definition for
‘%dopar%’
summarize_region_methylation: no visible binding for global variable
‘chunk’
summarize_region_methylation: no visible global function definition for
‘subsetByOverlaps’
Undefined global functions or variables:
%do% %dopar% IRanges TumourMethDatasets bg_file chunk
colorRampPalette column complete.cases cor data direction file_count
gene_transcripts is meth_site_plot_position meth_site_start
methodical_score mg name overlapsAny p.adjust pg pt queryHits
region_type seqlengths seqlevels setNames subsetByOverlaps transcript
transcript_name transcript_tss
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("methods", "is")
importFrom("stats", "complete.cases", "cor", "p.adjust", "pt",
"setNames")
importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to data() loading into the global environment:
File ‘methodical/R/download_datasets.R’:
data("TumourMethDatasets", package = "methodical")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'annotate_meth_site_plot.Rd':
\examples lines wider than 100 characters:
methodical::annotate_meth_site_plot(tubb6_correlation_plot, cpg_island_annotation, annotation_plot_height = 0.3)
Rd file 'calculate_meth_site_transcript_cors.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::calculate_meth_site_transcript_cors(meth_rse = tubb6_meth_rse,
transcript_expression_table = tubb6_transcript_counts, tss_gr = tubb6_tss, expand_upstream = 5000, expand_downstream = 5000)
Rd file 'calculate_region_methylation_transcript_cors.Rd':
\examples lines wider than 100 characters:
# Load TUBB6 TMRs, RangedSummarizedExperiment with methylation values for CpGs around TUBB6 TSS and TUBB6 transcript counts
genomic_regions = tubb6_tmrs, genomic_region_names = tubb6_tmrs$tmr_name, meth_rse = tubb6_meth_rse, transcript_expression_table = tu ... [TRUNCATED]
Rd file 'calculate_smoothed_methodical_scores.Rd':
\examples lines wider than 100 characters:
smoothed_methodical_scores = methodical::calculate_smoothed_methodical_scores(tubb6_cpg_meth_transcript_cors)
Rd file 'create_random_regions.Rd':
\examples lines wider than 100 characters:
random_regions = methodical::create_random_regions(genome = "BSgenome.Hsapiens.UCSC.hg38", n_regions = 10000)
Rd file 'extract_granges_meth_site_values.Rd':
\examples lines wider than 100 characters:
test_region_methylation = methodical::extract_granges_meth_site_values(tubb6_meth_rse, genomic_regions = test_region)
Rd file 'extract_meth_sites_from_genome.Rd':
\examples lines wider than 100 characters:
arabidopsis_cphpgs = methodical::extract_meth_sites_from_genome("BSgenome.Athaliana.TAIR.TAIR9", pattern = "CHG")
Rd file 'kallisto_index.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 'liftover_meth_rse.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 'plot_meth_site_values.Rd':
\examples lines wider than 100 characters:
methodical::plot_meth_site_values(tubb6_cpg_meth_transcript_cors, column_name = "cor", ylabel = "Spearman Correlation")
ylabel = "Spearman Correlation", reference_tss = attributes(tubb6_cpg_meth_transcript_cors)$tss_range)
Rd file 'plot_methodical_scores.Rd':
\examples lines wider than 100 characters:
methodical::plot_methodical_scores(tubb6_cpg_meth_transcript_cors, reference_tss = attributes(tubb6_cpg_meth_transcript_cors)$tss_range ... [TRUNCATED]
Rd file 'plot_tmrs.Rd':
\examples lines wider than 100 characters:
tubb6_correlation_plot = methodical::plot_meth_site_values(tubb6_cpg_meth_transcript_cors, column_name = "cor", ylabel = "Spearman Corr ... [TRUNCATED]
Rd file 'sample_meth_sites.Rd':
\examples lines wider than 100 characters:
random_cpgs = methodical::sample_meth_sites(tubb6_meth_rse, n_sites = 20, genomic_ranges_filter = mask_ranges,
Rd file 'summarize_region_methylation.Rd':
\examples lines wider than 100 characters:
test_gr = GRanges(c("chr18:12303400-12303500", "chr18:12303600-12303750", "chr18:12304000-12306000"))
test_gr_methylation = methodical::summarize_region_methylation(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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [232s/252s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
extract_meth_sites_from_genome 87.493 6.017 93.520
liftover_meth_rse 70.395 4.113 81.808
download_meth_dataset 10.333 1.849 18.086
make_meth_rse_from_array_files 6.201 0.173 6.380
annotate_meth_site_plot 5.306 0.243 12.318
* 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 ... [4s/5s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/methodical.Rcheck/00check.log’
for details.
===============================
BiocCheck('methodical_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.6
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpkYgeIi/file97bd5a054539/methodical
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpkYgeIi/file97bd6a226793
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3169/eb3920a8b574701dd57430efb442c72e4277035a/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 4.0 to 4.3.0.
* 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, GenomeWideAssociation
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...
* NOTE: Provide 'URL' field(s) 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...
* WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 15 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; 1121 lines (22%) are > 80
characters long.
* NOTE: Consider multiples of 4 spaces for line indents; 1663 lines
(32%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 17 NOTES
See the methodical.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir methodical_0.99.6.tar.gz'
>>>>>>>
* installing *source* package ‘methodical’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methodical)