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BioC 3.0: CHECK report for flowMatch on perceval

This page was generated on 2015-04-10 09:59:05 -0700 (Fri, 10 Apr 2015).

Package 312/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMatch 1.2.0
Ariful Azad
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/flowMatch
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: flowMatch
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowMatch_1.2.0.tar.gz
StartedAt: 2015-04-10 01:29:53 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:35:07 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 314.5 seconds
RetCode: 0
Status:  OK 
CheckDir: flowMatch.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowMatch_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowMatch.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 ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.2.0’
* 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 ‘flowMatch’ can be installed ... [28s/35s] 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 GNU extensions in Makefiles ... 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 ... [190s/191s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
create.template    26.557  0.347  27.083
Template-class     25.969  0.324  27.268
MetaCluster-class  24.937  0.318  25.313
flowMatch-package  24.511  0.283  24.826
template.tree      24.527  0.266  24.922
match.clusters     14.993  0.168  15.168
ClusterMatch-class 14.059  0.195  14.258
dist.template      12.059  0.140  12.220
* 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

flowMatch.Rcheck/00install.out:

* installing *source* package ‘flowMatch’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c BipartiteGraph.cpp -o BipartiteGraph.o
BipartiteGraph.cpp:18: warning: division by zero in ‘1.0e+0 / 0.’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MinWghtEdgCoverBipartite.cpp -o MinWghtEdgCoverBipartite.o
MinWghtEdgCoverBipartite.cpp: In function ‘void update_height(mclust&, std::vector<std::vector<templatePair, std::allocator<templatePair> >, std::allocator<std::vector<templatePair, std::allocator<templatePair> > > >, std::vector<std::vector<BipartiteGraph, std::allocator<BipartiteGraph> >, std::allocator<std::vector<BipartiteGraph, std::allocator<BipartiteGraph> > > >, double)’:
MinWghtEdgCoverBipartite.cpp:271: warning: comparison between signed and unsigned integer expressions
MinWghtEdgCoverBipartite.cpp: In function ‘classTemplate getTemplate(std::vector<std::vector<BipartiteGraph, std::allocator<BipartiteGraph> >, std::allocator<std::vector<BipartiteGraph, std::allocator<BipartiteGraph> > > >&, mclust&, int, double, double)’:
MinWghtEdgCoverBipartite.cpp:326: warning: unused variable ‘avgSample2TemplateCost’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c flowMatch.cpp -o flowMatch.o
flowMatch.cpp: In function ‘Rcpp::List computeMEC(Rcpp::NumericMatrix, double)’:
flowMatch.cpp:43: warning: comparison between signed and unsigned integer expressions
flowMatch.cpp:45: warning: comparison between signed and unsigned integer expressions
flowMatch.cpp:53: warning: comparison between signed and unsigned integer expressions
flowMatch.cpp:55: warning: comparison between signed and unsigned integer expressions
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 flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-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-class2.6600.0602.763
ClusterMatch-class14.059 0.19514.258
ClusteredSample-class2.2050.1652.498
MetaCluster-class24.937 0.31825.313
Template-class25.969 0.32427.268
create.template26.557 0.34727.083
dist.cluster1.6320.0491.682
dist.matrix2.9330.0472.982
dist.sample2.9570.0422.999
dist.template12.059 0.14012.220
flowMatch-package24.511 0.28324.826
mahalanobis.dist1.6150.0421.657
match.clusters14.993 0.16815.168
symmetric.KL1.5840.0291.614
template.tree24.527 0.26624.922