BioC 3.5: CHECK report for proFIA on malbec2

Package: proFIA

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings proFIA_1.2.0.tar.gz

StartedAt: 2017-08-16 01:24:00 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:29:32 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 331.8 seconds

RetCode: 0

Status:  OK

CheckDir: proFIA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings proFIA_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/proFIA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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                      104.328  1.436 105.870
getInjectionPeak                15.412  0.128  15.550
findFIAsignal                   14.052  0.204  14.266
estimateNoiseMS                  5.764  0.204   6.018
plotFlowgrams-proFIAset-method   5.480  0.020   5.507
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/proFIA.Rcheck/00check.log’
for details.

* installing *source* package ‘proFIA’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c FIABandsExtractionCentroid.c -o FIABandsExtractionCentroid.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c UtilFunc.c -o UtilFunc.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fastMatchPpm.c -o fastMatchPpm.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o proFIA.so FIABandsExtractionCentroid.o UtilFunc.o fastMatchPpm.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	0.084	0.000	0.166
analyzeAcquisitionFIA	0.012	0.000	0.014
determiningInjectionZone	0.916	0.020	0.992
determiningSizePeak.Geom	1.096	0.012	1.112
estimateNoiseMS	5.764	0.204	6.018
exportDataMatrix-proFIAset-method	0.016	0.000	0.015
exportExpressionSet-proFIAset-method	0.116	0.000	0.115
exportPeakTable-proFIAset-method	0.032	0.000	0.033
exportSampleMetadata-proFIAset-method	0.016	0.000	0.016
exportVariableMetadata-proFIAset-method	0.024	0.000	0.023
findBandsFIA	1.488	0.092	1.580
findFIAsignal	14.052	0.204	14.266
findMzGroup-proFIAset-method	0.032	0.000	0.044
getInjectionPeak	15.412	0.128	15.550
group.FIA-proFIAset-method	2.164	0.000	2.167
imputeMissingValues.WKNN_TN-proFIAset-method	0.548	0.000	0.550
makeDataMatrix-proFIAset-method	0.040	0.000	0.038
peaksGroup-proFIAset-method	0.040	0.000	0.037
plot	2.048	0.004	2.054
plotFlowgrams-proFIAset-method	5.480	0.020	5.507
plotNoise	0.216	0.000	0.217
plotRaw-proFIAset-method	1.880	0.024	1.906
plotSamplePeaks-proFIAset-method	0.020	0.000	0.021
proFIAset	104.328	1.436	105.870