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CHECK report for Rqc on merida1

This page was generated on 2019-04-16 11:58:08 -0400 (Tue, 16 Apr 2019).

Package 1347/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rqc 1.16.2
Welliton Souza
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Rqc
Branch: RELEASE_3_8
Last Commit: eb418ff
Last Changed Date: 2018-11-02 16:24:35 -0400 (Fri, 02 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Rqc
Version: 1.16.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rqc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rqc_1.16.2.tar.gz
StartedAt: 2019-04-16 02:30:08 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:36:28 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 380.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Rqc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rqc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rqc_1.16.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Rqc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.2’
* 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 ... 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 or elapsed time > 5s
              user system elapsed
Rqc-package 17.732  1.015  19.529
rqc         15.513  0.841  17.092
rqcReport   15.509  0.711  16.943
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Rqc.Rcheck/00check.log’
for details.



Installation output

Rqc.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rqc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Rqc’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RRDNA.cpp -o RRDNA.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -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 Rqc.so RRDNA.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (Rqc)

Tests output

Rqc.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:Biostrings':

    type

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: ggplot2
> 
> test_check("Rqc")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 27 SKIPPED: 0 FAILED: 0
Warning messages:
1: closing unused connection 5 (/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz) 
2: closing unused connection 4 (/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz) 
> 
> proc.time()
   user  system elapsed 
 21.364   0.934  22.663 

Example timings

Rqc.Rcheck/Rqc-Ex.timings

nameusersystemelapsed
Rqc-package17.732 1.01519.529
RqcResultSet-class0.0410.0010.044
checkpoint0.0030.0000.004
detectFileFormat0.0040.0010.004
fromRRDNA0.0020.0000.001
matdist0.0020.0010.001
rqc15.513 0.84117.092
rqcCycleAverageQualityPcaPlot0.3480.0020.352
rqcCycleAverageQualityPlot0.4200.0020.426
rqcCycleBaseCallsPlot0.7640.0040.772
rqcCycleGCPlot0.4280.0020.435
rqcCycleQualityBoxPlot3.2120.0073.256
rqcCycleQualityPlot1.0620.0141.086
rqcFileHeatmap0.2860.0020.290
rqcGroupCycleAverageQualityPlot0.3770.0020.382
rqcQA0.2700.0030.275
rqcReadFrequencyPlot0.3330.0010.335
rqcReadQualityBoxPlot0.3610.0010.362
rqcReadQualityPlot0.3180.0020.320
rqcReadWidthPlot0.3070.0010.309
rqcReport15.509 0.71116.943
rqcShinyReport0.0030.0000.004
stats4trim0.0940.0060.101
subsetByGroup0.6430.0700.717
subsetByPair0.0070.0010.007
toRRDNA0.0020.0000.002