Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:12 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the methrix package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1069/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methrix 1.4.07 (landing page) Anand Mayakonda
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: methrix |
Version: 1.4.07 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:methrix.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings methrix_1.4.07.tar.gz |
StartedAt: 2021-05-06 03:21:40 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 03:27:33 -0400 (Thu, 06 May 2021) |
EllapsedTime: 353.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methrix.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:methrix.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings methrix_1.4.07.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/methrix.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methrix/DESCRIPTION’ ... OK * this is package ‘methrix’ version ‘1.4.07’ * 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 ‘methrix’ 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 ... NOTE extract_CPGs: no visible global function definition for ‘standardChromosomes’ get_region_summary: no visible binding for global variable ‘..keep’ methrix_pca: no visible global function definition for ‘barplot’ methrix_pca: no visible global function definition for ‘points’ remove_snps: no visible global function definition for ‘seqlevelsStyle<-’ write_bigwigs: no visible global function definition for ‘seqlengths<-’ write_bigwigs: no visible global function definition for ‘seqlengths’ Undefined global functions or variables: ..keep barplot points seqlengths seqlengths<- seqlevelsStyle<- standardChromosomes Consider adding importFrom("graphics", "barplot", "points") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed remove_snps 7.252 0.192 8.761 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.12-bioc/meat/methrix.Rcheck/00check.log’ for details.
methrix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL methrix ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘methrix’ ... ** 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 (methrix)
methrix.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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(methrix) Loading required package: data.table Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift Loading required package: GenomeInfoDb 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:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("methrix") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ] > > proc.time() user system elapsed 31.624 0.560 32.220
methrix.Rcheck/methrix-Ex.timings
name | user | system | elapsed | |
convert_HDF5_methrix | 0.512 | 0.068 | 0.582 | |
convert_methrix | 0.288 | 0.020 | 0.310 | |
coverage_filter | 0.916 | 0.008 | 0.933 | |
extract_CPGs | 0.004 | 0.000 | 0.000 | |
get_matrix | 0.256 | 0.032 | 0.290 | |
get_region_summary | 0.300 | 0.024 | 0.314 | |
get_stats | 1.176 | 0.020 | 1.198 | |
load_HDF5_methrix | 0.588 | 0.024 | 0.613 | |
mask_methrix | 0.160 | 0.020 | 0.182 | |
methrix2bsseq | 0 | 0 | 0 | |
methrix_data | 0.040 | 0.016 | 0.055 | |
methrix_pca | 0.964 | 0.016 | 0.983 | |
methrix_report | 0.004 | 0.000 | 0.000 | |
order_by_sd | 0.056 | 0.012 | 0.070 | |
plot_coverage | 1.020 | 0.020 | 1.041 | |
plot_density | 1.940 | 0.020 | 1.958 | |
plot_pca | 0.992 | 0.024 | 1.022 | |
plot_stats | 1.304 | 0.016 | 1.321 | |
plot_violin | 1.032 | 0.012 | 1.046 | |
read_bedgraphs | 0.000 | 0.000 | 0.001 | |
region_filter | 0.040 | 0.016 | 0.056 | |
remove_snps | 7.252 | 0.192 | 8.761 | |
remove_uncovered | 0.992 | 0.016 | 1.007 | |
save_HDF5_methrix | 0.444 | 0.020 | 0.464 | |
subset_methrix | 0.052 | 0.024 | 0.074 | |
write_bedgraphs | 0.356 | 0.016 | 0.371 | |
write_bigwigs | 0.492 | 0.016 | 0.510 | |