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CHECK report for Rqc on tokay2

This page was generated on 2018-10-17 08:39:37 -0400 (Wed, 17 Oct 2018).

Package 1276/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rqc 1.14.0
Welliton Souza
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Rqc
Branch: RELEASE_3_7
Last Commit: 029044f
Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rqc
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rqc_1.14.0.tar.gz
StartedAt: 2018-10-17 04:33:08 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:41:27 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 499.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Rqc.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rqc_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rqc' version '1.14.0'
* 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 whether package 'Rqc' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:65: file link 'FastqFile' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:66: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rqc/libs/i386/Rqc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
Rqc-package 13.48   1.48   15.39
rqcReport   12.08   0.49   12.64
rqc         11.12   0.55   11.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
Rqc-package 12.64   0.56   13.39
rqc         12.17   0.50   12.78
rqcReport   11.47   0.39   11.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.Rcheck/00check.log'
for details.



Installation output

Rqc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Rqc_1.14.0.tar.gz && rm -rf Rqc.buildbin-libdir && mkdir Rqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rqc.buildbin-libdir Rqc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Rqc_1.14.0.zip && rm Rqc_1.14.0.tar.gz Rqc_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 56315  100 56315    0     0   984k      0 --:--:-- --:--:-- --:--:-- 1122k

install for i386

* installing *source* package 'Rqc' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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) {
                      ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rqc.dll tmp.def RRDNA.o RcppExports.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.buildbin-libdir/Rqc/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rqc'
    finding HTML links ... done
    Rqc-package                             html  
    RqcResultSet-class                      html  
    checkpoint                              html  
    detectFileFormat                        html  
    fromRRDNA                               html  
    matdist                                 html  
    rqc                                     html  
    finding level-2 HTML links ... done

    rqcCycleAverageQualityPcaPlot           html  
    rqcCycleAverageQualityPlot              html  
    rqcCycleBaseCallsPlot                   html  
    rqcCycleGCPlot                          html  
    rqcCycleQualityBoxPlot                  html  
    rqcCycleQualityPlot                     html  
    rqcFileHeatmap                          html  
    rqcGroupCycleAverageQualityPlot         html  
    rqcQA                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:65: file link 'FastqFile' in package 'ShortRead' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAl9IxC/R.INSTALL26d84ef61286/Rqc/man/rqcQA.Rd:66: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    rqcReadFrequencyPlot                    html  
    rqcReadQualityBoxPlot                   html  
    rqcReadQualityPlot                      html  
    rqcReadWidthPlot                        html  
    rqcReport                               html  
    rqcShinyReport                          html  
    stats4trim                              html  
    subsetByGroup                           html  
    subsetByPair                            html  
    toRRDNA                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Rqc' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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) {
                      ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rqc.dll tmp.def RRDNA.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rqc.buildbin-libdir/Rqc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rqc' as Rqc_1.14.0.zip
* DONE (Rqc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Rqc' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Rqc.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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: In if (is.null(value)) { :
  closing unused connection 5 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In if (is.null(value)) { :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
> 
> proc.time()
   user  system elapsed 
  15.32    1.90   17.21 

Rqc.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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: In sys.parent() :
  closing unused connection 5 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz)
2: In sys.parent() :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.7-bioc/R/library/ShortRead/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz)
> 
> proc.time()
   user  system elapsed 
  19.37    1.64   21.00 

Example timings

Rqc.Rcheck/examples_i386/Rqc-Ex.timings

nameusersystemelapsed
Rqc-package13.48 1.4815.39
RqcResultSet-class0.060.000.23
checkpoint000
detectFileFormat0.020.000.02
fromRRDNA000
matdist000
rqc11.12 0.5511.81
rqcCycleAverageQualityPcaPlot0.410.000.41
rqcCycleAverageQualityPlot0.640.000.64
rqcCycleBaseCallsPlot0.750.000.75
rqcCycleGCPlot0.290.000.30
rqcCycleQualityBoxPlot2.360.002.36
rqcCycleQualityPlot0.910.020.94
rqcFileHeatmap0.230.000.25
rqcGroupCycleAverageQualityPlot0.380.000.37
rqcQA0.230.000.23
rqcReadFrequencyPlot0.250.000.25
rqcReadQualityBoxPlot0.330.010.35
rqcReadQualityPlot0.360.000.36
rqcReadWidthPlot0.420.000.42
rqcReport12.08 0.4912.64
rqcShinyReport000
stats4trim0.090.000.09
subsetByGroup0.540.030.57
subsetByPair000
toRRDNA000

Rqc.Rcheck/examples_x64/Rqc-Ex.timings

nameusersystemelapsed
Rqc-package12.64 0.5613.39
RqcResultSet-class0.060.000.06
checkpoint000
detectFileFormat0.020.000.02
fromRRDNA000
matdist000
rqc12.17 0.5012.78
rqcCycleAverageQualityPcaPlot0.290.000.30
rqcCycleAverageQualityPlot0.380.000.38
rqcCycleBaseCallsPlot0.610.000.61
rqcCycleGCPlot0.330.000.33
rqcCycleQualityBoxPlot3.470.003.47
rqcCycleQualityPlot1.120.001.12
rqcFileHeatmap0.360.000.36
rqcGroupCycleAverageQualityPlot0.650.000.65
rqcQA0.330.000.33
rqcReadFrequencyPlot0.330.000.33
rqcReadQualityBoxPlot0.420.020.43
rqcReadQualityPlot0.470.000.55
rqcReadWidthPlot0.370.000.37
rqcReport11.47 0.3911.95
rqcShinyReport000
stats4trim0.080.000.08
subsetByGroup0.690.000.69
subsetByPair0.010.000.01
toRRDNA000