Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:54 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the Rqc package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1575/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rqc 1.24.0 (landing page) Welliton Souza
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: Rqc |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Rqc_1.24.0.tar.gz |
StartedAt: 2021-05-06 05:30:15 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 05:37:34 -0400 (Thu, 06 May 2021) |
EllapsedTime: 439.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rqc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Rqc_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Rqc.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 ‘Rqc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rqc’ version ‘1.24.0’ * 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: .travis.yml 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 ‘Rqc’ 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 Namespaces in Imports field not imported from: 'IRanges' 'Rcpp' All declared Imports should be used. * 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 Rqc-package 11.016 0.276 11.480 rqc 9.604 0.284 9.898 rqcReport 8.688 0.088 8.788 * 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 ‘/home/biocbuild/bbs-3.12-bioc/meat/Rqc.Rcheck/00check.log’ for details.
Rqc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Rqc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘Rqc’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RRDNA.cpp -o RRDNA.o RRDNA.cpp: In function ‘Rcpp::StringVector toRRDNA(Rcpp::StringVector)’: RRDNA.cpp:51:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0; j < dna.size(); j+=3) ~~^~~~~~~~~~~~ RRDNA.cpp: In function ‘Rcpp::StringVector fromRRDNA(Rcpp::StringVector)’: RRDNA.cpp:102:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(j = 1; j < rrdna.size(); ++j) { ~~^~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-Rqc/00new/Rqc/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 (Rqc)
Rqc.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(Rqc) Loading required package: BiocParallel Loading required package: ShortRead 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: Biostrings Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: GenomicAlignments 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: 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 Loading required package: ggplot2 > > test_check("Rqc") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ] Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (/home/biocbuild/bbs-3.12-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 4 (/home/biocbuild/bbs-3.12-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz) > > proc.time() user system elapsed 24.164 0.572 26.642
Rqc.Rcheck/Rqc-Ex.timings
name | user | system | elapsed | |
Rqc-package | 11.016 | 0.276 | 11.480 | |
RqcResultSet-class | 0.036 | 0.004 | 0.046 | |
checkpoint | 0.004 | 0.000 | 0.003 | |
detectFileFormat | 0.004 | 0.000 | 0.004 | |
fromRRDNA | 0.000 | 0.000 | 0.001 | |
matdist | 0.000 | 0.000 | 0.001 | |
rqc | 9.604 | 0.284 | 9.898 | |
rqcCycleAverageQualityPcaPlot | 0.196 | 0.000 | 0.196 | |
rqcCycleAverageQualityPlot | 0.332 | 0.000 | 0.331 | |
rqcCycleBaseCallsPlot | 0.420 | 0.000 | 0.418 | |
rqcCycleGCPlot | 0.296 | 0.000 | 0.298 | |
rqcCycleQualityBoxPlot | 1.912 | 0.000 | 1.915 | |
rqcCycleQualityPlot | 0.820 | 0.004 | 0.824 | |
rqcFileHeatmap | 0.140 | 0.000 | 0.137 | |
rqcGroupCycleAverageQualityPlot | 0.232 | 0.000 | 0.232 | |
rqcQA | 0.140 | 0.000 | 0.139 | |
rqcReadFrequencyPlot | 0.136 | 0.000 | 0.137 | |
rqcReadQualityBoxPlot | 0.176 | 0.000 | 0.174 | |
rqcReadQualityPlot | 0.136 | 0.004 | 0.139 | |
rqcReadWidthPlot | 0.180 | 0.000 | 0.179 | |
rqcReport | 8.688 | 0.088 | 8.788 | |
rqcShinyReport | 0.004 | 0.000 | 0.005 | |
stats4trim | 0.124 | 0.008 | 0.134 | |
subsetByGroup | 0.852 | 0.108 | 0.964 | |
subsetByPair | 0.000 | 0.008 | 0.008 | |
toRRDNA | 0 | 0 | 0 | |