nebbiolo2 Summary
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| Package: methodical |
| Version: 0.99.0 |
| 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 52.86 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/methodical_20231006145408/methodical.install-out.txt methodical_0.99.0.tar.gz && BiocCheck('methodical_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 48.58 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 7095.97 KiB |
| BuildID:: methodical_20231006145408 |
| 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: 1. |
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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘methodical/inst/extdata/tubb6_meth_rse/se.rds’
* building ‘methodical_0.99.0.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('methodical')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3169/methodical_20231006145408/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/methodical_20231006145408/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 ‘0.99.0’
* 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
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’
chunk_regions: no visible global function definition for
‘subsetByOverlaps’
create_meth_rse_from_hdf5: no visible global function definition for
‘setNames’
create_random_regions: no visible global function definition for
‘seqlengths’
create_random_regions: no visible global function definition for
‘overlapsAny’
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
‘seqlevels’
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’
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’
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’
write_chunks_to_hdf5: no visible binding for global variable ‘chunk’
Undefined global functions or variables:
%do% %dopar% IRanges bg_file chunk colorRampPalette column
complete.cases cor 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")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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_islands, 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$tmr_name, meth_rse = tubb6_meth_rse, transcript_table = tubb6_transcr ... [TRUNCATED]
Rd file 'calculate_smoothed_methodical_scores.Rd':
\examples lines wider than 100 characters:
smoothed_methodical_scores = methodical::calculate_smoothed_methodical_scores(tubb6_cpg_meth_transcript_cors)
Rd file 'create_random_regions.Rd':
\examples lines wider than 100 characters:
random_regions = methodical::create_random_regions(genome = "BSgenome.Hsapiens.UCSC.hg38", n_regions = 10000)
Rd file 'extract_granges_meth_site_values.Rd':
\examples lines wider than 100 characters:
test_region_methylation = methodical::extract_granges_meth_site_values(tubb6_meth_rse, genomic_regions = test_region)
Rd file 'extract_meth_sites_from_genome.Rd':
\examples lines wider than 100 characters:
arabidopsis_cphpgs = methodical::extract_meth_sites_from_genome("BSgenome.Athaliana.TAIR.TAIR9", pattern = "CHG")
Rd file 'kallisto_index.Rd':
\examples lines wider than 100 characters:
download.file("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz")
Rd file 'liftover_meth_rse.Rd':
\examples lines wider than 100 characters:
# Liftover tubb6_meth_rse from hg38 to hg19, keeping only sites that were mapped to CpG sites in hg19
Rd file 'plot_meth_site_values.Rd':
\examples lines wider than 100 characters:
methodical::plot_meth_site_values(tubb6_cpg_meth_transcript_cors, column_name = "cor", ylabel = "Spearman Correlation")
ylabel = "Spearman Correlation", reference_region = attributes(tubb6_cpg_meth_transcript_cors)$tss_range)
Rd file 'plot_methodical_scores.Rd':
\examples lines wider than 100 characters:
methodical::plot_methodical_scores(tubb6_cpg_meth_transcript_cors, reference_region = attributes(tubb6_cpg_meth_transcript_cors)$tss_ra ... [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 files in ‘vignettes’ ... OK
* checking examples ... [168s/186s] ERROR
Running examples in ‘methodical-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: liftover_meth_rse
> ### Title: Liftover rowRanges of a RangedSummarizedExperiment for
> ### methylation data from one genome build to another
> ### Aliases: liftover_meth_rse
>
> ### ** Examples
>
> # Load sample RangedSummarizedExperiment with CpG methylation data
> data(tubb6_meth_rse, package = "methodical"); tubb6_meth_rse = eval(tubb6_meth_rse)
>
> # Get CpG sites for hg19
> hg19_cpgs = methodical::extract_meth_sites_from_genome("BSgenome.Hsapiens.UCSC.hg19")
Error in .stopOnAvailablePkg(genome) :
BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Calls: <Anonymous> ... .getBSgenomeObjectFromInstalledPkgname -> .stopOnAvailablePkg
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3169/methodical_20231006145408/methodical.Rcheck/00check.log’
for details.
===============================
BiocCheck('methodical_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpeGomY4/file18a6221eae1c9b/methodical
─ installDir: /tmp/RtmpeGomY4/file18a6222c6249ba
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3169/methodical_20231006145408/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 3.5.0 to 4.3.0.
* Checking package size...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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 12 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; 1068 lines (23%) are > 80
characters long.
* NOTE: Consider multiples of 4 spaces for line indents; 1538 lines
(33%) 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 ──
1 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
[top]
| Package: methodical |
| Version: 0.99.0 |
| 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 40.07 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/methodical_20231006145408/methodical.install-out.txt methodical_0.99.0.tar.gz && BiocCheck('methodical_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 13 minutes 4.76 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh methodical_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 24.08 seconds |
| PackageFileSize: 7142.67 KiB |
| BuildID:: methodical_20231006145408 |
| 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: 1. 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘methodical/inst/extdata/tubb6_meth_rse/se.rds’
* building ‘methodical_0.99.0.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('methodical')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3169/methodical_20231006145408/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/methodical_20231006145408/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 ‘0.99.0’
* 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [18s/18s] NOTE
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’
chunk_regions: no visible global function definition for
‘subsetByOverlaps’
create_meth_rse_from_hdf5: no visible global function definition for
‘setNames’
create_random_regions: no visible global function definition for
‘seqlengths’
create_random_regions: no visible global function definition for
‘overlapsAny’
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
‘seqlevels’
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’
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’
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’
write_chunks_to_hdf5: no visible binding for global variable ‘chunk’
Undefined global functions or variables:
%do% %dopar% IRanges bg_file chunk colorRampPalette column
complete.cases cor 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")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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_islands, 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_table = tubb6_transcr ... [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_region = attributes(tubb6_cpg_meth_transcript_cors)$tss_range)
Rd file 'plot_methodical_scores.Rd':
\examples lines wider than 100 characters:
methodical::plot_methodical_scores(tubb6_cpg_meth_transcript_cors, reference_region = attributes(tubb6_cpg_meth_transcript_cors)$tss_ra ... [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 files in ‘vignettes’ ... OK
* checking examples ... [10m/11m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_meth_rse_from_bedgraphs 286.554 30.948 357.887
extract_meth_sites_from_genome 89.469 8.569 101.137
liftover_meth_rse 87.770 9.429 117.419
make_meth_rse_from_array_files 10.147 0.379 10.550
annotate_meth_site_plot 6.938 0.465 24.873
summarize_region_methylation 5.735 0.038 5.785
* 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 ... [6s/7s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3169/methodical_20231006145408/methodical.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('methodical_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: methodical
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp6catHD/file93ce1e8fd01d/methodical
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp6catHD/file93ce26cc9dd3
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3169/methodical_20231006145408/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 3.5.0 to 4.3.0.
* Checking package size...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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 12 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; 1068 lines (23%) are > 80
characters long.
* NOTE: Consider multiples of 4 spaces for line indents; 1538 lines
(33%) 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 ──
1 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_0.99.0.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)