BioC 3.3: CHECK report for Rqc on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rqc_1.5.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rqc.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.3’
* 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 ... [28s/28s] 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 ... [61s/59s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
Rqc-package 15.207  0.468  14.934
rqcReport   13.981  0.328  13.302
rqc         13.798  0.347  13.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/11s]
 [12s/12s] 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rqc.Rcheck/00check.log’
for details.

* installing *source* package ‘Rqc’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RRDNA.cpp -o RRDNA.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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 /Users/biocbuild/bbs-3.3-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)

name	user	system	elapsed
Rqc-package	15.207	0.468	14.934
RqcResultSet-class	0.043	0.002	0.045
checkpoint	0.004	0.000	0.004
detectFileFormat	0.005	0.001	0.005
fromRRDNA	0.001	0.000	0.001
matdist	0.001	0.001	0.001
rqc	13.798	0.347	13.325
rqcCycleAverageQualityPcaPlot	0.258	0.001	0.259
rqcCycleAverageQualityPlot	0.375	0.001	0.377
rqcCycleBaseCallsPlot	0.503	0.001	0.504
rqcCycleGCPlot	0.249	0.001	0.249
rqcCycleQualityBoxPlot	2.715	0.029	2.746
rqcCycleQualityPlot	0.833	0.007	0.840
rqcFileHeatmap	0.192	0.002	0.196
rqcGroupCycleAverageQualityPlot	0.379	0.007	0.386
rqcQA	0.235	0.001	0.237
rqcReadFrequencyPlot	0.227	0.001	0.228
rqcReadQualityBoxPlot	0.310	0.000	0.311
rqcReadQualityPlot	0.268	0.000	0.269
rqcReadWidthPlot	0.274	0.000	0.275
rqcReport	13.981	0.328	13.302
rqcShinyReport	0.002	0.001	0.002
stats4trim	0.100	0.004	0.105
subsetByGroup	0.580	0.044	0.624
subsetByPair	0.006	0.000	0.007
toRRDNA	0.001	0.000	0.001

BioC 3.3: CHECK report for Rqc on morelia

Summary

Command output