flowMatch 1.6.0
Ariful Azad
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/flowMatch | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings flowMatch_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/flowMatch.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.6.0’
* 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 ... [23s/24s] 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 ... [114s/114s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
create.template 16.494 0.024 16.543
Template-class 16.400 0.040 16.464
flowMatch-package 15.214 0.012 15.280
MetaCluster-class 14.966 0.008 15.012
template.tree 14.420 0.008 14.445
ClusterMatch-class 9.154 0.027 9.186
match.clusters 8.756 0.004 8.775
dist.template 7.209 0.004 7.209
* 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-3.2-bioc/meat/flowMatch.Rcheck/00check.log’
for details.
* installing *source* package ‘flowMatch’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c BipartiteGraph.cpp -o BipartiteGraph.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)