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BioC 3.0: CHECK report for cn.farms on perceval

This page was generated on 2015-04-10 09:55:43 -0700 (Fri, 10 Apr 2015).

Package 171/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.14.0
Andreas Mitterecker
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/cn.farms
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: cn.farms
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.farms_1.14.0.tar.gz
StartedAt: 2015-04-10 00:03:01 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:08:42 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 341.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.farms_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/cn.farms.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 ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cn.farms’ can be installed ... [24s/58s] 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
initializeBigMatrix: no visible global function definition for
  ‘isPackageLoaded’
* 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 R/sysdata.rda ... 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 ... [28s/35s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

cn.farms.Rcheck/00install.out:

* installing *source* package ‘cn.farms’ ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
laplace.cpp:442: warning: unused variable ‘method’
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 sparse_farms.c -o sparse_farms.o
llvm-g++-4.2 -arch x86_64 -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 cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

cn.farms.Rcheck/cn.farms-Ex.timings:

nameusersystemelapsed
cn.farms0.0010.0000.001
combineData1.6340.0522.276
createAnnotation0.0010.0010.001
distributionDistance0.1530.0100.180
dnaCopySf0.1560.0040.160
fragLengCorr3.8340.0464.252
mlSummarization4.4020.1944.857
normalizeAverage0.0020.0000.002
normalizeCels0.0010.0000.001
normalizeNpData0.0010.0000.001
plotDendrogram0.5890.0181.343
plotDensity0.4770.0200.601
plotEvalIc0.4840.0300.816
plotRegions0.1840.0141.347
plotSmoothScatter1.1390.0351.784
plotViolines0.1580.0040.290
slSummarization3.8940.0794.230
sparseFarmsC0.0010.0000.002
summarizeFarmsExact0.0080.0030.010
summarizeFarmsExact20.0080.0020.010
summarizeFarmsExact30.0070.0020.009
summarizeFarmsGaussian0.0040.0000.004
summarizeFarmsMethods0.0040.0010.003
summarizeFarmsVariational0.0040.0010.005
summarizeWindowBps0.0080.0000.009
summarizeWindowMethods0.0030.0000.003
summarizeWindowStd0.0050.0010.006