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BioC 2.14: CHECK report for flowMatch on morelia

This page was generated on 2014-10-08 09:07:15 -0700 (Wed, 08 Oct 2014).

Package 285/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMatch 1.1.2
Ariful Azad
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowMatch
Last Changed Rev: 93254 / Revision: 95116
Last Changed Date: 2014-08-08 12:21:11 -0700 (Fri, 08 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: flowMatch
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowMatch_1.1.2.tar.gz
StartedAt: 2014-10-07 22:46:49 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:50:49 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 239.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowMatch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowMatch_1.1.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/flowMatch.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.1.2’
* 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 ‘flowMatch’ can be installed ... [24s/24s] 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [151s/152s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
create.template    22.319  0.215  22.588
Template-class     21.442  0.192  21.673
flowMatch-package  20.167  0.173  20.619
MetaCluster-class  19.689  0.161  19.927
template.tree      18.523  0.157  18.691
ClusterMatch-class 11.718  0.111  12.014
match.clusters     11.470  0.110  11.592
dist.template       9.166  0.079   9.270
* 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

flowMatch.Rcheck/00install.out:

* installing *source* package ‘flowMatch’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c BipartiteGraph.cpp -o BipartiteGraph.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c MinWghtEdgCoverBipartite.cpp -o MinWghtEdgCoverBipartite.o
MinWghtEdgCoverBipartite.cpp:326:9: warning: unused variable 'avgSample2TemplateCost' [-Wunused-variable]
        double avgSample2TemplateCost;
               ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c flowMatch.cpp -o flowMatch.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/flowMatch.Rcheck/flowMatch/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 (flowMatch)

flowMatch.Rcheck/flowMatch-Ex.timings:

nameusersystemelapsed
Cluster-class1.7750.0281.848
ClusterMatch-class11.718 0.11112.014
ClusteredSample-class1.8250.0961.945
MetaCluster-class19.689 0.16119.927
Template-class21.442 0.19221.673
create.template22.319 0.21522.588
dist.cluster1.3680.0221.392
dist.matrix2.3260.0292.357
dist.sample2.1030.0332.136
dist.template9.1660.0799.270
flowMatch-package20.167 0.17320.619
mahalanobis.dist1.2880.0221.313
match.clusters11.470 0.11011.592
symmetric.KL1.2720.0201.292
template.tree18.523 0.15718.691