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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the NanoMethViz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoMethViz.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 1244/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoMethViz 1.2.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: NanoMethViz |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoMethViz_1.2.0.tar.gz |
StartedAt: 2021-10-14 21:38:40 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:46:21 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 460.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoMethViz_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/NanoMethViz.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 ‘NanoMethViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoMethViz’ version ‘1.2.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘NanoMethViz’ 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 ... NOTE 'library' or 'require' calls in package code: ‘Homo.sapiens’ ‘Mus.musculus’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 use of PKG_*FLAGS in Makefiles ... 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 get_exons_homo_sapiens 20.880 1.292 22.302 get_exons_mus_musculus 20.389 0.837 21.270 plot_gene_heatmap 7.191 0.107 7.311 plot_region_heatmap 6.937 0.090 7.033 NanoMethResult-class 6.018 0.618 6.649 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/NanoMethViz.Rcheck/00check.log’ for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-NanoMethViz/00new/NanoMethViz/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 (NanoMethViz)
NanoMethViz.Rcheck/tests/testthat.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. > library(testthat) > library(NanoMethViz) Loading required package: ggplot2 > > test_check("NanoMethViz") Loading required package: Mus.musculus Loading required package: AnnotationDbi 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.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:NanoMethViz': samples Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: OrganismDbi Loading required package: GenomicFeatures Loading required package: GenomeInfoDb Loading required package: GenomicRanges Attaching package: 'GenomicFeatures' The following object is masked from 'package:NanoMethViz': exons Loading required package: GO.db Loading required package: org.Mm.eg.db Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene [2021-10-14 21:45:39] creating intermediate files... [2021-10-14 21:45:39] parsing chr11... [2021-10-14 21:45:39] parsing chr12... [2021-10-14 21:45:39] parsing chr18... [2021-10-14 21:45:39] parsing chr5... [2021-10-14 21:45:39] parsing chr7... [2021-10-14 21:45:39] parsing chrX... [2021-10-14 21:45:39] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 [2021-10-14 21:45:39] creating bsseq object... [2021-10-14 21:45:39] reading in parsed data... [2021-10-14 21:45:40] constructing matrices... [2021-10-14 21:45:40] done [2021-10-14 21:45:40] creating intermediate files... [2021-10-14 21:45:40] parsing chr11... [2021-10-14 21:45:41] parsing chr12... [2021-10-14 21:45:41] parsing chr18... [2021-10-14 21:45:41] parsing chr5... [2021-10-14 21:45:41] parsing chr7... [2021-10-14 21:45:41] parsing chrX... [2021-10-14 21:45:41] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 [2021-10-14 21:45:41] creating bsseq object... [2021-10-14 21:45:41] reading in parsed data... [2021-10-14 21:45:41] constructing matrices... [2021-10-14 21:45:42] done [2021-10-14 21:45:42] creating intermediate files... [2021-10-14 21:45:42] parsing chr11... [2021-10-14 21:45:42] parsing chr12... [2021-10-14 21:45:42] parsing chr18... [2021-10-14 21:45:43] parsing chr5... [2021-10-14 21:45:43] parsing chr7... [2021-10-14 21:45:43] parsing chrX... [2021-10-14 21:45:43] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 [2021-10-14 21:45:43] creating bsseq object... [2021-10-14 21:45:43] reading in parsed data... [2021-10-14 21:45:43] constructing matrices... [2021-10-14 21:45:45] done processing /Library/Frameworks/R.framework/Versions/4.1/Resources/library/NanoMethViz/sample1_nanopolish.tsv.gz... guessing file is produced by nanopolish... processing /Library/Frameworks/R.framework/Versions/4.1/Resources/library/NanoMethViz/sample2_nanopolish.tsv.gz... guessing file is produced by nanopolish... [2021-10-14 21:46:10] sorting methylation table [2021-10-14 21:46:10] compressing methylation table to tabix with index [2021-10-14 21:46:10] creating intermediate files... [2021-10-14 21:46:10] parsing chr1... [2021-10-14 21:46:10] parsing chr2... [2021-10-14 21:46:10] parsing chr3... [2021-10-14 21:46:10] parsing chr4... [2021-10-14 21:46:10] parsing chr5... [2021-10-14 21:46:10] parsing chr6... [2021-10-14 21:46:10] parsing chr7... [2021-10-14 21:46:10] parsing chr8... [2021-10-14 21:46:10] parsing chr9... [2021-10-14 21:46:10] parsing chr10... [2021-10-14 21:46:10] parsing chr11... [2021-10-14 21:46:10] parsing chr12... [2021-10-14 21:46:10] parsing chr13... [2021-10-14 21:46:10] parsing chr14... [2021-10-14 21:46:10] parsing chr15... [2021-10-14 21:46:10] parsing chr16... [2021-10-14 21:46:10] parsing chr17... [2021-10-14 21:46:10] parsing chr18... [2021-10-14 21:46:10] parsing chr19... [2021-10-14 21:46:10] parsing chrM... [2021-10-14 21:46:10] parsing chrX... [2021-10-14 21:46:10] parsing chrY... [2021-10-14 21:46:10] samples found: B6Cast_Prom_3_cast B6Cast_Prom_2_bl6 B6Cast_Prom_3_bl6 B6Cast_Prom_1_cast B6Cast_Prom_2_cast B6Cast_Prom_1_bl6 sample1_nanopolish.tsv sample2_nanopolish.tsv [2021-10-14 21:46:10] creating bsseq object... [2021-10-14 21:46:10] reading in parsed data... [2021-10-14 21:46:10] constructing matrices... [2021-10-14 21:46:11] done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ] > > proc.time() user system elapsed 54.298 1.895 56.076
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 6.018 | 0.618 | 6.649 | |
bsseq_to_edger | 1.288 | 0.047 | 1.322 | |
bsseq_to_log_methy_ratio | 1.208 | 0.037 | 1.221 | |
create_tabix_file | 0.233 | 0.025 | 0.258 | |
exons | 0.003 | 0.001 | 0.003 | |
exons_to_genes | 0.724 | 0.020 | 0.744 | |
get_example_exons_mus_musculus | 0.836 | 0.027 | 0.864 | |
get_exons_homo_sapiens | 20.880 | 1.292 | 22.302 | |
get_exons_mus_musculus | 20.389 | 0.837 | 21.270 | |
load_example_nanomethresult | 0.850 | 0.024 | 0.873 | |
methy | 0.001 | 0.000 | 0.001 | |
methy_col_names | 0 | 0 | 0 | |
methy_to_bsseq | 1.611 | 0.027 | 1.583 | |
plot_agg_regions | 2.639 | 0.055 | 2.696 | |
plot_agg_regions_sample_grouped | 2.852 | 0.152 | 3.006 | |
plot_gene | 3.271 | 0.069 | 3.346 | |
plot_gene_heatmap | 7.191 | 0.107 | 7.311 | |
plot_grange | 1.984 | 0.043 | 2.031 | |
plot_grange_heatmap | 3.705 | 0.049 | 3.758 | |
plot_region | 3.497 | 0.055 | 3.557 | |
plot_region_heatmap | 6.937 | 0.090 | 7.033 | |
query_methy | 1.047 | 0.028 | 1.075 | |
samples | 0.001 | 0.001 | 0.001 | |