Daniel Huebschmann
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: RELEASE_3_11 |
| Last Commit: 2e86384 |
| Last Changed Date: 2020-04-27 15:01:09 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:00 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE YAPSA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1900/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.14.0 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: YAPSA |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings YAPSA_1.14.0.tar.gz |
| StartedAt: 2020-10-17 09:18:29 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 09:30:52 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 742.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: YAPSA.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings YAPSA_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/YAPSA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '1.14.0'
* 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 whether package 'YAPSA' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:169: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:172: file link 'LCD_complex_cutoff_consensus' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:173: file link 'LCD_complex_cutoff_combined' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:174: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:177: file link 'LCD_complex_cutoff_combined' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:179: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:180: file link 'LCD_complex_cutoff_consensus' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:104: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/annotation_exposures_barplot.Rd:56: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/annotation_exposures_list_barplot.Rd:59: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/confidence_indel_calulation.Rd:40: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/confidence_indel_only_calulation.Rd:32: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:50: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:52: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:25: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:29: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:87: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:89: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_df.Rd:50: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_df.Rd:54: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:23: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:25: file link 'SomaticSignatures' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:11: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:18: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/plotExchangeSpectra.Rd:38: file link 'theme_grey' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/plotExchangeSpectra_indel.Rd:37: file link 'theme_grey' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/read_entry.Rd:50: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/read_entry.Rd:52: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:42: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:53: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:54: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:64: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:35: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:46: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:47: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:57: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/translate_to_hg19.Rd:31: file link 'BSgenome.Hsapiens.UCSC.hg19' in package 'BSgenome.Hsapiens.UCSC.hg19' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/YAPSA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
confidence_indel_only_calulation 18.87 0.05 18.92
create_indel_mutation_catalogue_from_df 11.81 0.49 12.29
build_gene_list_for_pathway 8.68 1.73 25.96
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
confidence_indel_only_calulation 18.84 0.00 18.84
create_indel_mutation_catalogue_from_df 12.30 0.47 12.76
build_gene_list_for_pathway 10.24 0.04 25.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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 ... OK
* DONE
Status: 1 WARNING
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/YAPSA.Rcheck/00check.log'
for details.
YAPSA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/YAPSA_1.14.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.14.0.zip && rm YAPSA_1.14.0.tar.gz YAPSA_1.14.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1483k 100 1483k 0 0 18.1M 0 --:--:-- --:--:-- --:--:-- 19.8M
install for i386
* installing *source* package 'YAPSA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'YAPSA'
finding HTML links ... done
GenomeOfNl_raw html
LCD html
LCD_SMC html
LCD_complex_cutoff html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:169: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:172: file link 'LCD_complex_cutoff_consensus' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:173: file link 'LCD_complex_cutoff_combined' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:174: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:177: file link 'LCD_complex_cutoff_combined' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:179: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:180: file link 'LCD_complex_cutoff_consensus' in package 'YAPSA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/LCD_complex_cutoff.Rd:104: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
MutCat_indel_df html
SMC html
SMC_perPID html
YAPSA html
add_annotation html
add_as_fist_to_list html
aggregate_exposures_by_category html
annotate_intermut_dist_PID html
annotate_intermut_dist_cohort html
annotation_exposures_barplot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/annotation_exposures_barplot.Rd:56: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
annotation_exposures_list_barplot html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/annotation_exposures_list_barplot.Rd:59: file link 'draw' in package 'ComplexHeatmap' does not exist and so has been treated as a topic
annotation_heatmap_exposures html
attribute_nucleotide_exchanges html
attribute_sequence_contex_indel html
attribution_of_indels html
build_gene_list_for_pathway html
classify_indels html
compare_SMCs html
compare_exposures html
compare_expousre_sets html
compare_sets html
compare_to_catalogues html
complex_heatmap_exposures html
computeLogLik html
compute_comparison_stat_df html
confIntExp html
confidence_indel_calulation html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/confidence_indel_calulation.Rd:40: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
confidence_indel_only_calulation html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/confidence_indel_only_calulation.Rd:32: file link 'LCD_complex_cutoff_perPID' in package 'YAPSA' does not exist and so has been treated as a topic
correct_rounded html
cosineDist html
cosineMatchDist html
create_indel_mut_cat_from_df html
create_indel_mutation_catalogue_from_df
html
create_mutation_catalogue_from_VR html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:50: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:52: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:25: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:29: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:87: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_VR.Rd:89: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
create_mutation_catalogue_from_df html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_df.Rd:50: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/create_mutation_catalogue_from_df.Rd:54: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
cut_breaks_as_intervals html
cutoffs html
cutoffs_pcawg html
deriveSigInd_df html
disambiguateVector html
enrichSigs html
exampleINDEL_YAPSA html
exampleYAPSA html
exchange_colour_vector html
exome_mutCatRaw_df html
exposures_barplot html
extract_names_from_gene_list html
find_affected_PIDs html
getSequenceContext html
get_extreme_PIDs html
hclust_exposures html
logLikelihood html
lymphomaNature2013_mutCat_df html
makeVRangesFromDataFrame html
make_catalogue_strata_df html
make_comparison_matrix html
make_strata_df html
make_subgroups_df html
melt_exposures html
merge_exposures html
normalizeMotifs_otherRownames html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:23: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:25: file link 'SomaticSignatures' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:11: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/normalizeMotifs_otherRownames.Rd:18: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
normalize_df_per_dim html
plotExchangeSpectra html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/plotExchangeSpectra.Rd:38: file link 'theme_grey' in package 'ggplot2' does not exist and so has been treated as a topic
plotExchangeSpectra_indel html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/plotExchangeSpectra_indel.Rd:37: file link 'theme_grey' in package 'ggplot2' does not exist and so has been treated as a topic
plotExposuresConfidence html
plotExposuresConfidence_indel html
plot_SMC html
plot_exposures html
plot_strata html
read_entry html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/read_entry.Rd:50: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/read_entry.Rd:52: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic
relateSigs html
repeat_df html
round_precision html
run_SMC html
run_annotate_vcf_pl html
run_comparison_catalogues html
run_comparison_general html
run_kmer_frequency_correction html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:42: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:53: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:54: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_correction.Rd:64: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
run_kmer_frequency_normalization html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:35: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:46: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:47: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/run_kmer_frequency_normalization.Rd:57: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
run_plot_strata_general html
shapiro_if_possible html
sigs html
sigs_pcawg html
split_exposures_by_subgroups html
stat_plot_subgroups html
stat_test_SMC html
stat_test_subgroups html
stderrmean html
sum_over_list_of_df html
targetCapture_cor_factors html
temp_trellis_rainfall_plot html
testSigs html
test_exposureAffected html
test_gene_list_in_exposures html
transform_rownames_R_to_MATLAB html
translate_to_hg19 html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpmKJ1jj/R.INSTALL2e981fbe780e/YAPSA/man/translate_to_hg19.Rd:31: file link 'BSgenome.Hsapiens.UCSC.hg19' in package 'BSgenome.Hsapiens.UCSC.hg19' does not exist and so has been treated as a topic
trellis_rainfall_plot html
trellis_rainfall_plot_old html
variateExp html
variateExpSingle html
** 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
install for x64
* installing *source* package 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.14.0.zip
* DONE (YAPSA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked
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YAPSA.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS=" ")
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
>
> test_check("YAPSA")
YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand information missing, set to "+".
YAPSA:::makeVRangesFromDataFrame::in_PID.field found. Retrieving PID information.
YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found. Retrieving subgroup information.
== testthat results ===========================================================
[ OK: 62 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.03 2.06 20.37
|
YAPSA.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS=" ")
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
>
> test_check("YAPSA")
YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand information missing, set to "+".
YAPSA:::makeVRangesFromDataFrame::in_PID.field found. Retrieving PID information.
YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found. Retrieving subgroup information.
== testthat results ===========================================================
[ OK: 62 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.68 0.64 18.64
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YAPSA.Rcheck/examples_i386/YAPSA-Ex.timings
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YAPSA.Rcheck/examples_x64/YAPSA-Ex.timings
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