BioC 3.4: CHECK report for TargetSearch on morelia

Package: TargetSearch

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TargetSearch_1.30.0.tar.gz

StartedAt: 2017-04-15 08:46:20 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:47:23 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 63.4 seconds

RetCode: 0

Status:  OK

CheckDir: TargetSearch.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 TargetSearch_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TargetSearch.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘1.30.0’
* 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 ‘TargetSearch’ 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 ... NOTE
ProfileCleanUp: no visible global function definition for ‘as.dist’
plotPeak: no visible global function definition for ‘mtext’
plotPeak: no visible global function definition for ‘rect’
plotPeak: no visible global function definition for ‘gray’
plotPeak: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  as.dist gray matlines mtext rect
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "matlines", "mtext", "rect")
  importFrom("stats", "as.dist")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... 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
RIcorrect 10.375    0.7  12.059
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.

* installing *source* package ‘TargetSearch’ ...
** 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 Rinit.c -o Rinit.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 file.c -o file.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 find_peaks.c -o find_peaks.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 getLine.c -o getLine.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 hpf.c -o hpf.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 ncdf.c -o ncdf.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 netcdf_peak_finding.c -o netcdf_peak_finding.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 peakExtraction.c -o peakExtraction.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 ppc.c -o ppc.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 TargetSearch.so Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/TargetSearch.Rcheck/TargetSearch/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 (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.060	0.007	0.103
FindPeaks	0.536	0.019	0.656
ImportFameSettings	0.007	0.001	0.016
ImportLibrary	0.019	0.002	0.020
ImportSamples	0.004	0.001	0.022
NetCDFPeakFinding	0.343	0.025	0.498
Profile	1.681	0.062	1.745
ProfileCleanUp	1.733	0.050	1.781
RIcorrect	10.375	0.700	12.059
fixRI	1.198	0.084	1.281
medianRILib	1.113	0.033	1.147
peakFind	0.537	0.017	0.555
plotFAME	0.017	0.003	0.020
plotPeak	0.262	0.025	0.285
plotPeakSimple	0.405	0.032	0.437
plotRIdev	0.689	0.032	0.723
plotSpectra	0.542	0.013	0.556
quantMatrix	1.640	0.054	1.696
ri2rt	0.007	0.001	0.008
riMatrix	0.946	0.071	1.017
rt2ri	0.006	0.001	0.007
sampleRI	1.050	0.028	1.077
tsLib-class	0.007	0.001	0.009
tsMSdata-class	0.001	0.000	0.002
tsProfile-class	0.001	0.000	0.001
tsRim-class	0.002	0.000	0.002
tsSample-class	0.015	0.002	0.016
writeLibText	0.033	0.003	0.035