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BioC 3.5: CHECK report for TargetSearch on malbec2

This page was generated on 2017-08-16 13:13:21 -0400 (Wed, 16 Aug 2017).

Package 1305/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TargetSearch 1.32.0
Alvaro Cuadros-Inostroza
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/TargetSearch
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TargetSearch
Version: 1.32.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.32.0.tar.gz
StartedAt: 2017-08-16 02:36:30 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:37:18 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 48.3 seconds
RetCode: 0
Status:  OK 
CheckDir: TargetSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TargetSearch_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/TargetSearch.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 ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘1.32.0’
* 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 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 8.12  0.288    8.54
* 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-3.5-bioc/meat/TargetSearch.Rcheck/00check.log’
for details.


TargetSearch.Rcheck/00install.out:

* installing *source* package ‘TargetSearch’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c file.c -o file.o
gcc -I/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c getLine.c -o getLine.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hpf.c -o hpf.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ncdf.c -o ncdf.o
gcc -I/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c peakExtraction.c -o peakExtraction.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ppc.c -o ppc.o
gcc -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)

TargetSearch.Rcheck/TargetSearch-Ex.timings:

nameusersystemelapsed
FAMEoutliers0.1200.0040.155
FindPeaks0.2840.0160.333
ImportFameSettings0.0120.0000.012
ImportLibrary0.0200.0000.021
ImportSamples0.0040.0000.005
NetCDFPeakFinding1.2000.0361.270
Profile1.2480.0201.267
ProfileCleanUp1.1000.0281.130
RIcorrect8.1200.2888.540
fixRI0.8200.0320.850
medianRILib0.4680.0000.471
peakFind0.2520.0040.257
plotFAME0.0120.0000.010
plotPeak0.1240.0200.143
plotPeakSimple0.3720.0160.388
plotRIdev0.3840.0080.391
plotSpectra0.240.000.24
quantMatrix0.8080.0120.819
ri2rt0.0040.0000.004
riMatrix0.6320.0120.645
rt2ri0.0040.0000.004
sampleRI0.4640.0120.474
tsLib-class0.0080.0000.005
tsMSdata-class0.0000.0000.001
tsProfile-class0.0000.0000.001
tsRim-class0.0000.0000.001
tsSample-class0.0280.0000.028
writeLibText0.0200.0040.024