BioC 3.5: CHECK report for proFIA on toluca2

Package: proFIA

Version: 1.1.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proFIA_1.1.10.tar.gz

StartedAt: 2017-04-23 08:12:29 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:19:44 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 434.8 seconds

RetCode: 0

Status:  OK

CheckDir: proFIA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proFIA_1.1.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/proFIA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proFIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proFIA’ version ‘1.1.10’
* 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:
  .BBSoptions
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 ‘proFIA’ 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 ... 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
proFIAset                      152.841  5.922 159.954
findFIAsignal                   18.385  0.888  19.373
estimateNoiseMS                  6.783  0.754   7.564
plotFlowgrams-proFIAset-method   5.372  0.129   5.563
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/proFIA.Rcheck/00check.log’
for details.

* installing *source* package ‘proFIA’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c UtilFunc.c -o UtilFunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c fastMatchPpm.c -o fastMatchPpm.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 proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/proFIA.Rcheck/proFIA/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 (proFIA)

name	user	system	elapsed
acquisitionDirectory	0.066	0.003	0.071
analyzeAcquisitionFIA	0.015	0.001	0.015
determiningInjectionZone	1.007	0.028	1.039
determiningSizePeak.Geom	1.392	0.020	1.417
estimateNoiseMS	6.783	0.754	7.564
exportDataMatrix-proFIAset-method	0.020	0.002	0.022
exportExpressionSet-proFIAset-method	0.178	0.002	0.181
exportPeakTable-proFIAset-method	0.048	0.002	0.051
exportSampleMetadata-proFIAset-method	0.024	0.002	0.026
exportVariableMetadata-proFIAset-method	0.030	0.002	0.033
findBandsFIA	1.597	0.290	1.899
findFIAsignal	18.385	0.888	19.373
findMzGroup-proFIAset-method	0.033	0.003	0.036
getInjectionPeak	4.197	0.407	4.627
group.FIA-proFIAset-method	3.030	0.121	3.173
imputeMissingValues.WKNN_TN-proFIAset-method	0.863	0.022	0.888
makeDataMatrix-proFIAset-method	0.045	0.001	0.046
peaksGroup-proFIAset-method	0.056	0.003	0.059
plot	3.463	0.017	3.519
plotFlowgrams-proFIAset-method	5.372	0.129	5.563
plotNoise	0.377	0.002	0.386
plotRaw-proFIAset-method	1.945	0.041	2.006
plotSamplePeaks-proFIAset-method	0.026	0.003	0.029
proFIAset	152.841	5.922	159.954