Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the epialleleR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epialleleR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 579/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epialleleR 1.0.0 (landing page) Oleksii Nikolaienko
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: epialleleR |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epialleleR_1.0.0.tar.gz |
StartedAt: 2021-10-14 18:45:09 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:52:00 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 411.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: epialleleR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epialleleR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/epialleleR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘epialleleR/DESCRIPTION’ ... OK * this is package ‘epialleleR’ version ‘1.0.0’ * 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 ‘epialleleR’ can be installed ... OK * 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 * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generateVcfReport 32.4 0.307 33.395 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/epialleleR.Rcheck/00check.log’ for details.
epialleleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL epialleleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘epialleleR’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_apply_cigar.cpp -o rcpp_apply_cigar.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_char_to_context.cpp -o rcpp_char_to_context.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_cx_report.cpp -o rcpp_cx_report.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_match_target.cpp -o rcpp_match_target.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_merge_ends.cpp -o rcpp_merge_ends.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o epialleleR.so RcppExports.o rcpp_apply_cigar.o rcpp_char_to_context.o rcpp_cx_report.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_merge_ends.o rcpp_threshold_reads.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-epialleleR/00new/epialleleR/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (epialleleR)
epialleleR.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > BiocGenerics:::testPackage("epialleleR") Reading BED file [0.085s] Reading BAM file [1.125s] Preprocessing BAM data: Transforming sequences [0.029s] Merging pairs [0.019s] Computing ECDFs for within- and out-of-context per-read beta values [0.066s] Reading BED file [0.029s] Reading BAM file [0.236s] Preprocessing BAM data: Transforming sequences [0.011s] Merging pairs [0.011s] Computing ECDFs for within- and out-of-context per-read beta values [0.011s] Reading BED file [0.031s] Reading BAM file [0.223s] Preprocessing BAM data: Transforming sequences [0.010s] Merging pairs [0.011s] Preparing amplicon report [0.076s] Reading BED file [0.019s] Reading BAM file [0.146s] Preprocessing BAM data: Transforming sequences [0.007s] Merging pairs [0.008s] Thresholding reads [0.001s] Preparing amplicon report [0.019s] Writing the report [0.002s] Reading BAM file [0.224s] Preprocessing BAM data: Transforming sequences [0.019s] Merging pairs [0.019s] Thresholding reads [0.002s] Preparing cytosine report [0.045s] Reading BAM file [0.186s] Preprocessing BAM data: Transforming sequences [0.019s] Merging pairs [0.019s] Thresholding reads [0.004s] Preparing cytosine report [0.038s] Writing the report [0.003s] Reading BED file [0.020s] Reading VCF file [1.444s] Reading BAM file [0.145s] Preprocessing BAM data: Transforming sequences [0.010s] Merging pairs [0.010s] Extracting base frequences [0.158s] Already preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect. Reading BAM file [0.248s] Preprocessing BAM data: Transforming sequences [0.028s] Merging pairs [0.025s] Thresholding reads [0.004s] Extracting base frequences [16.760s] Writing the report [0.012s] Already preprocessed BAM supplied as an input. Options 'min.mapq' and 'skip.duplicates' will have no effect. RUNIT TEST PROTOCOL -- Thu Oct 14 18:51:50 2021 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : epialleleR RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 60.113 1.252 62.569
epialleleR.Rcheck/epialleleR-Ex.timings
name | user | system | elapsed | |
generateBedEcdf | 1.309 | 0.053 | 1.366 | |
generateBedReport | 0.960 | 0.050 | 1.013 | |
generateCytosineReport | 1.277 | 0.036 | 1.313 | |
generateVcfReport | 32.400 | 0.307 | 33.395 | |
preprocessBam | 0.278 | 0.009 | 0.288 | |