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BioC 3.1: CHECK report for flowMatch on zin2

This page was generated on 2015-10-09 09:25:51 -0700 (Fri, 09 Oct 2015).

Package 337/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMatch 1.4.0
Ariful Azad
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/flowMatch
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowMatch
Version: 1.4.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings flowMatch_1.4.0.tar.gz
StartedAt: 2015-10-09 01:13:02 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:16:21 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 198.9 seconds
RetCode: 0
Status:  OK 
CheckDir: flowMatch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings flowMatch_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/flowMatch.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 ... [22s/26s] OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
* 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 ... [108s/127s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Template-class     15.595  0.004  18.063
create.template    15.465  0.035  18.614
MetaCluster-class  14.598  0.031  18.295
flowMatch-package  14.161  0.011  15.717
template.tree      13.649  0.004  16.803
ClusterMatch-class  8.553  0.023   9.720
match.clusters      8.289  0.000  10.291
dist.template       6.837  0.012   7.371
* 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/flowMatch.Rcheck/00check.log’
for details.


flowMatch.Rcheck/00install.out:

* installing *source* package ‘flowMatch’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c BipartiteGraph.cpp -o BipartiteGraph.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c MinWghtEdgCoverBipartite.cpp -o MinWghtEdgCoverBipartite.o
MinWghtEdgCoverBipartite.cpp: In function ‘void update_height(mclust&, std::vector<std::vector<templatePair> >, std::vector<std::vector<BipartiteGraph> >, double)’:
MinWghtEdgCoverBipartite.cpp:271:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i<tree.height.size(); i++)
                                  ^
MinWghtEdgCoverBipartite.cpp: In function ‘void computeDegConsistencyNew(std::vector<std::vector<templatePair> >&, std::vector<std::vector<BipartiteGraph> >&, double, double)’:
MinWghtEdgCoverBipartite.cpp:487:10: warning: variable ‘delta_cx_cy’ set but not used [-Wunused-but-set-variable]
      int delta_cx_cy  = 0;
          ^
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c flowMatch.cpp -o flowMatch.o
flowMatch.cpp: In function ‘Rcpp::List computeMEC(Rcpp::NumericMatrix, double)’:
flowMatch.cpp:43:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i<mec.sCoverVecVec.size(); i++)
                                       ^
flowMatch.cpp:45:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j=0; j<mec.sCoverVecVec[i].size(); j++)
                                           ^
flowMatch.cpp:53:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i<mec.tCoverVecVec.size(); i++)
                                       ^
flowMatch.cpp:55:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j=0; j<mec.tCoverVecVec[i].size(); j++)
                                           ^
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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-class1.2140.0041.345
ClusterMatch-class8.5530.0239.720
ClusteredSample-class1.6800.0311.835
MetaCluster-class14.598 0.03118.295
Template-class15.595 0.00418.063
create.template15.465 0.03518.614
dist.cluster0.9210.0080.978
dist.matrix1.7430.0001.794
dist.sample1.7240.0001.873
dist.template6.8370.0127.371
flowMatch-package14.161 0.01115.717
mahalanobis.dist0.9520.0001.409
match.clusters 8.289 0.00010.291
symmetric.KL0.9380.0000.978
template.tree13.649 0.00416.803