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BioC 3.4: CHECK report for Rqc on zin1

This page was generated on 2016-09-21 03:39:27 -0700 (Wed, 21 Sep 2016).

Package 1050/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rqc 1.7.2
Welliton Souza
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rqc
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rqc
Version: 1.7.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.7.2.tar.gz
StartedAt: 2016-09-20 12:04:19 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:08:57 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 277.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Rqc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rqc_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Rqc.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.7.2’
* 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 ... OK
* 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 loading without being on the library search path ... 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
.ui.Rqc: no visible global function definition for 'packageVersion'
rqc: no visible global function definition for 'browseURL'
rqcCycleAverageQualityPcaCalc: no visible global function definition
  for 'prcomp'
rqcFileHeatmap: no visible global function definition for 'hclust'
stats4trim : <anonymous>: no visible global function definition for
  'head'
Undefined global functions or variables:
  browseURL hclust head packageVersion prcomp
Consider adding
  importFrom("stats", "hclust", "prcomp")
  importFrom("utils", "browseURL", "head", "packageVersion")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 13.740  1.252  14.049
rqc         12.956  1.308  13.333
rqcReport   11.936  1.232  12.144
* 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-3.4-bioc/meat/Rqc.Rcheck/00check.log’
for details.


Rqc.Rcheck/00install.out:

* installing *source* package ‘Rqc’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/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++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o Rqc.so RRDNA.o RcppExports.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/Rqc.Rcheck/Rqc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rqc)

Rqc.Rcheck/Rqc-Ex.timings:

nameusersystemelapsed
Rqc-package13.740 1.25214.049
RqcResultSet-class0.0320.0040.036
checkpoint0.0040.0000.003
detectFileFormat0.0040.0000.003
fromRRDNA0.0000.0000.002
matdist0.0000.0040.000
rqc12.956 1.30813.333
rqcCycleAverageQualityPcaPlot0.2680.0200.290
rqcCycleAverageQualityPlot0.3160.0040.322
rqcCycleBaseCallsPlot0.5160.0080.522
rqcCycleGCPlot0.2520.0000.252
rqcCycleQualityBoxPlot2.3360.0042.340
rqcCycleQualityPlot0.7120.0040.718
rqcFileHeatmap0.1880.0000.188
rqcGroupCycleAverageQualityPlot0.3280.0000.336
rqcQA0.1840.0000.185
rqcReadFrequencyPlot0.1880.0000.187
rqcReadQualityBoxPlot0.2640.0000.262
rqcReadQualityPlot0.1840.0000.183
rqcReadWidthPlot0.2320.0000.231
rqcReport11.936 1.23212.144
rqcShinyReport0.0040.0000.003
stats4trim0.10.00.1
subsetByGroup0.4760.0200.495
subsetByPair0.0080.0000.009
toRRDNA0.0000.0000.001