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CHECK report for Rqc on malbec2

This page was generated on 2019-10-16 12:05:44 -0400 (Wed, 16 Oct 2019).

Package 1415/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rqc 1.18.0
Welliton Souza
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Rqc
Branch: RELEASE_3_9
Last Commit: d8a92f7
Last Changed Date: 2019-05-02 11:53:50 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  TIMEOUT  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rqc
Version: 1.18.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rqc_1.18.0.tar.gz
StartedAt: 2019-10-16 04:40:43 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:46:06 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 323.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Rqc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rqc.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rqc_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rqc.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 or elapsed time > 5s
              user system elapsed
Rqc-package 12.321  0.228  12.861
rqcReport    9.775  0.084   9.865
rqc          9.526  0.208   9.739
* 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-3.9-bioc/meat/Rqc.Rcheck/00check.log’
for details.



Installation output

Rqc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rqc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Rqc’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)

Tests output

Rqc.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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, rowsum

Loading required package: ggplot2
> 
> test_check("Rqc")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning messages:
1: In if (S3Case) class1 <- class1[[1L]] :
  closing unused connection 5 (/home/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In if (S3Case) class1 <- class1[[1L]] :
  closing unused connection 4 (/home/biocbuild/bbs-3.9-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
> 
> proc.time()
   user  system elapsed 
 20.289   0.782  21.061 

Example timings

Rqc.Rcheck/Rqc-Ex.timings

nameusersystemelapsed
Rqc-package12.321 0.22812.861
RqcResultSet-class0.0390.0000.095
checkpoint0.0040.0000.003
detectFileFormat0.0040.0000.004
fromRRDNA0.0010.0000.001
matdist0.0000.0000.001
rqc9.5260.2089.739
rqcCycleAverageQualityPcaPlot0.2560.0000.256
rqcCycleAverageQualityPlot0.2860.0000.286
rqcCycleBaseCallsPlot0.4680.0000.468
rqcCycleGCPlot0.3840.0000.384
rqcCycleQualityBoxPlot1.4270.0001.427
rqcCycleQualityPlot0.8580.0080.866
rqcFileHeatmap0.2070.0040.212
rqcGroupCycleAverageQualityPlot0.2810.0000.280
rqcQA0.20.00.2
rqcReadFrequencyPlot0.1910.0000.191
rqcReadQualityBoxPlot0.3240.0000.324
rqcReadQualityPlot0.3370.0000.338
rqcReadWidthPlot0.3630.0000.363
rqcReport9.7750.0849.865
rqcShinyReport0.0000.0040.005
stats4trim0.1200.0120.131
subsetByGroup0.6270.0190.646
subsetByPair0.0060.0000.005
toRRDNA0.0010.0000.002