Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.12: CHECK report for cn.farms on george2

This page was generated on 2013-10-09 09:37:42 -0700 (Wed, 09 Oct 2013).

Package 133/671HostnameOS / ArchBUILDCHECKBUILD BIN
cn.farms 1.8.0
Andreas Mitterecker
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/cn.farms
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: cn.farms
Version: 1.8.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.8.0.tar.gz
StartedAt: 2013-10-09 01:03:00 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:08:20 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 319.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.8.0’
* 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 ... [28s/32s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [37s/39s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mlSummarization 7.224  0.168   7.629
slSummarization 5.993  0.056   6.132
fragLengCorr    5.085  0.012   5.397
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

cn.farms.Rcheck/00install.out:

* installing *source* package ‘cn.farms’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:6: warning: unused variable ‘method’ [-Wunused-variable]
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:368:57: warning: ‘I1right’ may be used uninitialized in this function [-Wuninitialized]
laplace.cpp:367:53: warning: ‘I1left’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
combineData2.3560.0802.467
createAnnotation0.0080.0040.010
distributionDistance0.7280.0080.737
dnaCopySf0.2040.0040.227
fragLengCorr5.0850.0125.397
mlSummarization7.2240.1687.629
normalizeAverage0.0200.0000.019
normalizeCels0.0200.0000.017
normalizeNpData0.0280.0000.028
plotDendrogram0.2160.0080.225
plotDensity0.8200.0160.833
plotEvalIc1.0360.0121.050
plotRegions0.2320.0040.236
plotSmoothScatter0.9480.0120.959
plotViolines0.2240.0000.223
slSummarization5.9930.0566.132
sparseFarmsC0.0120.0000.012
summarizeFarmsExact0.0200.0000.019
summarizeFarmsExact20.0120.0080.020
summarizeFarmsExact30.0160.0040.020
summarizeFarmsGaussian0.0160.0000.014
summarizeFarmsMethods0.0120.0000.014
summarizeFarmsVariational0.0160.0000.015
summarizeWindowBps0.0240.0000.024
summarizeWindowMethods0.0160.0000.015
summarizeWindowStd0.0240.0040.029