BioC 3.5: CHECK report for proFIA on veracruz2

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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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/proFIA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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:
  .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                      119.026  3.114 126.030
findFIAsignal                   14.956  0.645  16.067
estimateNoiseMS                  6.014  0.663   6.858
plotFlowgrams-proFIAset-method   5.043  0.128   5.308
* 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   -fPIC  -Wall -g -O2  -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c UtilFunc.c -o UtilFunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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	0.063	0.003	0.071
analyzeAcquisitionFIA	0.013	0.001	0.014
determiningInjectionZone	0.960	0.027	1.007
determiningSizePeak.Geom	1.271	0.024	1.336
estimateNoiseMS	6.014	0.663	6.858
exportDataMatrix-proFIAset-method	0.020	0.001	0.023
exportExpressionSet-proFIAset-method	0.158	0.003	0.165
exportPeakTable-proFIAset-method	0.038	0.002	0.041
exportSampleMetadata-proFIAset-method	0.020	0.002	0.021
exportVariableMetadata-proFIAset-method	0.021	0.002	0.024
findBandsFIA	1.661	0.268	1.988
findFIAsignal	14.956	0.645	16.067
findMzGroup-proFIAset-method	0.036	0.003	0.040
getInjectionPeak	3.842	0.229	4.191
group.FIA-proFIAset-method	2.871	0.039	3.005
imputeMissingValues.WKNN_TN-proFIAset-method	0.742	0.012	0.776
makeDataMatrix-proFIAset-method	0.046	0.002	0.049
peaksGroup-proFIAset-method	0.056	0.004	0.061
plot	3.144	0.032	3.260
plotFlowgrams-proFIAset-method	5.043	0.128	5.308
plotNoise	0.262	0.003	0.270
plotRaw-proFIAset-method	1.839	0.042	1.944
plotSamplePeaks-proFIAset-method	0.016	0.002	0.019
proFIAset	119.026	3.114	126.030

BioC 3.5: CHECK report for proFIA on veracruz2

Summary

Command output