BioC 3.6: CHECK report for proFIA on veracruz1

Package: proFIA

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proFIA_1.3.2.tar.gz

StartedAt: 2017-08-16 06:59:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:04:47 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 325.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: proFIA.Rcheck

Warnings: 1

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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_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/proFIA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.2’
* 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 ... 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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                            87.420  2.177  92.030
findFIAsignal                        13.988  0.528  14.868
impute.FIA-proFIAset-method           7.358  0.138   7.703
impute.randomForest-proFIAset-method  6.005  0.120   6.316
estimateNoiseMS                       5.202  0.561   5.958
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-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-3.6-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	0.055	0.004	0.067
analyzeAcquisitionFIA	0.015	0.002	0.016
determiningInjectionZone	0.815	0.027	0.866
determiningSizePeak.Geom	0.972	0.020	1.026
estimateNoiseMS	5.202	0.561	5.958
exportDataMatrix-proFIAset-method	0.020	0.002	0.022
exportExpressionSet-proFIAset-method	0.138	0.001	0.141
exportPeakTable-proFIAset-method	0.035	0.001	0.038
exportSampleMetadata-proFIAset-method	0.016	0.002	0.019
exportVariableMetadata-proFIAset-method	0.015	0.001	0.016
findBandsFIA	1.394	0.238	1.667
findFIAsignal	13.988	0.528	14.868
findMzGroup-proFIAset-method	0.029	0.003	0.032
getInjectionPeak	2.780	0.216	3.085
group.FIA-proFIAset-method	2.447	0.042	2.596
impute.FIA-proFIAset-method	7.358	0.138	7.703
impute.KNN_TN-proFIAset-method	0.540	0.007	0.567
impute.randomForest-proFIAset-method	6.005	0.120	6.316
makeDataMatrix-proFIAset-method	0.049	0.002	0.050
peaksGroup-proFIAset-method	0.044	0.003	0.047
plot	3.107	0.013	3.228
plotFlowgrams-proFIAset-method	4.484	0.096	4.687
plotNoise	0.319	0.003	0.333
plotRaw-proFIAset-method	1.717	0.038	1.822
plotSamplePeaks-proFIAset-method	0.020	0.002	0.023
proFIAset	87.420	2.177	92.030