BioC 3.4: CHECK report for TargetSearch on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.29.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TargetSearch.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.29.1’
* 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 8.38   0.46   8.922
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.

* installing *source* package ‘TargetSearch’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c file.c -o file.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c find_peaks.c -o find_peaks.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c getLine.c -o getLine.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hpf.c -o hpf.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ncdf.c -o ncdf.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c netcdf_peak_finding.c -o netcdf_peak_finding.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c peakExtraction.c -o peakExtraction.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ppc.c -o ppc.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/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 -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
* DONE (TargetSearch)

name	user	system	elapsed
FAMEoutliers	0.052	0.004	0.090
FindPeaks	0.256	0.008	0.496
ImportFameSettings	0.008	0.000	0.011
ImportLibrary	0.012	0.000	0.018
ImportSamples	0.004	0.000	0.007
NetCDFPeakFinding	0.292	0.008	0.307
Profile	0.824	0.016	0.836
ProfileCleanUp	0.780	0.016	0.795
RIcorrect	8.380	0.460	8.922
fixRI	0.796	0.028	0.824
medianRILib	0.456	0.024	0.480
peakFind	0.260	0.004	0.261
plotFAME	0.008	0.004	0.012
plotPeak	0.200	0.000	0.201
plotPeakSimple	0.304	0.044	0.346
plotRIdev	0.388	0.008	0.394
plotSpectra	0.256	0.000	0.256
quantMatrix	0.788	0.028	0.813
ri2rt	0.004	0.000	0.004
riMatrix	0.668	0.016	0.683
rt2ri	0.004	0.000	0.004
sampleRI	0.480	0.012	0.492
tsLib-class	0.004	0.004	0.005
tsMSdata-class	0.000	0.000	0.001
tsProfile-class	0.000	0.000	0.001
tsRim-class	0.000	0.000	0.002
tsSample-class	0.008	0.000	0.010
writeLibText	0.032	0.000	0.031

BioC 3.4: CHECK report for TargetSearch on zin1

Summary

Command output