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BioC 3.0: CHECK report for flagme on perceval

This page was generated on 2015-04-10 09:54:16 -0700 (Fri, 10 Apr 2015).

Package 296/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.22.0
Mark Robinson , Riccardo Romoli
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flagme
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: flagme
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flagme_1.22.0.tar.gz
StartedAt: 2015-04-10 01:20:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:23:56 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 196.5 seconds
RetCode: 0
Status:  OK 
CheckDir: flagme.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flagme_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/flagme.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.22.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘gcspikelite’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flagme’ can be installed ... [14s/16s] 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 loading without being on the library search path ... 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
addXCMSPeaks : <anonymous>: no visible global function definition for
  ‘xcmsSet’
* 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
parseChromaTOF 5.507  0.031   5.557
addXCMSPeaks   4.871  0.119   5.055
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/flagme.Rcheck/00check.log’
for details.

flagme.Rcheck/00install.out:

* installing *source* package ‘flagme’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c dp.c -o dp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o flagme.so dp.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘flagme’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flagme)

flagme.Rcheck/flagme-Ex.timings:

nameusersystemelapsed
addAMDISPeaks1.1470.0741.645
addChromaTOFPeaks0.4240.0200.444
addXCMSPeaks4.8710.1195.055
betweenAlignment000
calcTimeDiffs1.3420.1031.466
clusterAlignment1.2700.0831.353
compress1.5070.0431.550
dp1.2690.0461.316
gatherInfo1.5840.0461.631
imputePeaks2.1940.0872.286
multipleAlignment1.6460.0511.698
normDotProduct1.2920.0461.338
parseChromaTOF5.5070.0315.557
parseELU3.9710.0223.995
peaksAlignment0.0000.0000.001
peaksDataset1.0970.0551.152
plot0.6860.0770.763
plotImage0.4390.0310.475
progressiveAlignment1.5810.0581.640
rmaFitUnit1.3350.0471.383