BioC 3.5: CHECK report for proFIA on oaxaca

Package: proFIA

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings proFIA_1.1.3.tar.gz

StartedAt: 2017-03-04 07:19:08 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:24:16 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 308.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: proFIA.Rcheck

Warnings: 2

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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_1.1.3.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 r72177)
* 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 ‘1.1.3’
* 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 ... 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 ... WARNING
Missing link or links in documentation object 'findBandsFIA.Rd':
  ‘determiningInjectionZone’

Missing link or links in documentation object 'findFIAsignal.Rd':
  ‘determiningInjectionZone’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘determiningInjectionZone’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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       72.098  5.442  77.569
findFIAsignal   10.682  0.778  11.483
estimateNoiseMS  4.836  0.741   5.625
* 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: 2 WARNINGs, 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	0.063	0.005	0.179
analyzeAcquisitionFIA	0.016	0.001	0.017
determiningSizePeak.Geom	0.630	0.033	0.721
estimateNoiseMS	4.836	0.741	5.625
exportDataMatrix-proFIAset-method	0.021	0.003	0.025
exportExpressionSet-proFIAset-method	0.203	0.006	0.210
exportPeakTable-proFIAset-method	0.047	0.002	0.049
exportSampleMetadata-proFIAset-method	0.025	0.002	0.028
exportVariableMetadata-proFIAset-method	0.030	0.002	0.033
fillPeaks.WKNN-proFIAset-method	0.064	0.005	0.088
findBandsFIA	1.342	0.304	1.649
findFIAsignal	10.682	0.778	11.483
findMzGroup-proFIAset-method	0.067	0.003	0.103
getInjectionPeak	2.087	0.339	2.428
group.FIA-proFIAset-method	2.767	0.101	2.870
makeDataMatrix-proFIAset-method	0.028	0.002	0.030
peaksGroup-proFIAset-method	0.075	0.004	0.078
plotEICs-proFIAset-method	2.885	0.105	3.151
plotInjectionPeaks-proFIAset-method	0.022	0.002	0.024
plotNoise	0.415	0.003	0.418
plotRaw-proFIAset-method	1.146	0.036	1.182
proFIAset	72.098	5.442	77.569