BioC 3.3: CHECK report for flowMatch on moscato2
This page was generated on 2016-10-13 12:52:08 -0700 (Thu, 13 Oct 2016).
flowMatch 1.8.0
Ariful Azad
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/flowMatch | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: flowMatch
|
| Version: 1.8.0
|
| Command: rm -rf flowMatch.buildbin-libdir flowMatch.Rcheck && mkdir flowMatch.buildbin-libdir flowMatch.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowMatch.buildbin-libdir flowMatch_1.8.0.tar.gz >flowMatch.Rcheck\00install.out 2>&1 && cp flowMatch.Rcheck\00install.out flowMatch-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=flowMatch.buildbin-libdir --install="check:flowMatch-install.out" --force-multiarch --no-vignettes --timings flowMatch_1.8.0.tar.gz
|
| StartedAt: 2016-10-13 03:49:24 -0700 (Thu, 13 Oct 2016)
|
| EndedAt: 2016-10-13 03:58:02 -0700 (Thu, 13 Oct 2016)
|
| EllapsedTime: 517.9 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: flowMatch.Rcheck
|
| Warnings: 0
|
Command output
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### Running command:
###
### rm -rf flowMatch.buildbin-libdir flowMatch.Rcheck && mkdir flowMatch.buildbin-libdir flowMatch.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowMatch.buildbin-libdir flowMatch_1.8.0.tar.gz >flowMatch.Rcheck\00install.out 2>&1 && cp flowMatch.Rcheck\00install.out flowMatch-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=flowMatch.buildbin-libdir --install="check:flowMatch-install.out" --force-multiarch --no-vignettes --timings flowMatch_1.8.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/flowMatch.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowMatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowMatch' 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 whether package 'flowMatch' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
doc 3.6Mb
libs 1.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
ClusteredSample: no visible global function definition for 'cov'
ellipse: no visible global function definition for 'qchisq'
ellipse: no visible global function definition for 'lines'
limitcalc: no visible global function definition for 'qchisq'
plot.cluster.contours: no visible global function definition for 'par'
plot.cluster.contours: no visible global function definition for
'plot.new'
plot.cluster.contours: no visible global function definition for
'mtext'
template.tree,Template: no visible global function definition for
'as.dendrogram'
Undefined global functions or variables:
as.dendrogram cov lines mtext par plot.new qchisq
Consider adding
importFrom("graphics", "lines", "mtext", "par", "plot.new")
importFrom("stats", "as.dendrogram", "cov", "qchisq")
to your NAMESPACE file.
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/flowMatch.buildbin-libdir/flowMatch/libs/i386/flowMatch.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
create.template 25.60 0.06 25.68
template.tree 24.95 0.11 25.06
flowMatch-package 22.20 0.05 22.28
Template-class 20.97 0.05 21.01
MetaCluster-class 19.51 0.09 19.77
match.clusters 14.72 0.06 14.77
ClusterMatch-class 13.20 0.06 13.26
dist.template 11.31 0.03 11.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
create.template 25.36 0.03 25.55
MetaCluster-class 25.07 0.05 25.16
Template-class 24.31 0.06 24.98
template.tree 22.92 0.05 22.97
flowMatch-package 22.74 0.03 22.78
match.clusters 14.60 0.02 15.21
ClusterMatch-class 13.79 0.02 13.81
dist.template 10.78 0.00 10.78
* 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: 3 NOTEs
See
'E:/biocbld/bbs-3.3-bioc/meat/flowMatch.Rcheck/00check.log'
for details.
flowMatch.Rcheck/00install.out:
install for i386
* installing *source* package 'flowMatch' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c BipartiteGraph.cpp -o BipartiteGraph.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:271:16: 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;
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c flowMatch.cpp -o flowMatch.o
flowMatch.cpp: In function 'Rcpp::List computeMEC(Rcpp::NumericMatrix, double)':
flowMatch.cpp:43:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<mec.sCoverVecVec.size(); i++)
^
flowMatch.cpp:45:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0; j<mec.sCoverVecVec[i].size(); j++)
^
flowMatch.cpp:53:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<mec.tCoverVecVec.size(); i++)
^
flowMatch.cpp:55:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0; j<mec.tCoverVecVec[i].size(); j++)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowMatch.dll tmp.def BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/flowMatch.buildbin-libdir/flowMatch/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'flowMatch' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c BipartiteGraph.cpp -o BipartiteGraph.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:271:16: 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;
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c flowMatch.cpp -o flowMatch.o
flowMatch.cpp: In function 'Rcpp::List computeMEC(Rcpp::NumericMatrix, double)':
flowMatch.cpp:43:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<mec.sCoverVecVec.size(); i++)
^
flowMatch.cpp:45:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0; j<mec.sCoverVecVec[i].size(); j++)
^
flowMatch.cpp:53:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0; i<mec.tCoverVecVec.size(); i++)
^
flowMatch.cpp:55:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0; j<mec.tCoverVecVec[i].size(); j++)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowMatch.dll tmp.def BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/flowMatch.buildbin-libdir/flowMatch/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowMatch' as flowMatch_1.8.0.zip
* DONE (flowMatch)
flowMatch.Rcheck/examples_i386/flowMatch-Ex.timings:
| name | user | system | elapsed
|
| Cluster-class | 1.72 | 0.00 | 4.74 |
|
| ClusterMatch-class | 13.20 | 0.06 | 13.26 |
|
| ClusteredSample-class | 2.65 | 0.08 | 2.73 |
|
| MetaCluster-class | 19.51 | 0.09 | 19.77 |
|
| Template-class | 20.97 | 0.05 | 21.01 |
|
| create.template | 25.60 | 0.06 | 25.68 |
|
| dist.cluster | 1.56 | 0.03 | 1.59 |
|
| dist.matrix | 2.57 | 0.00 | 2.57 |
|
| dist.sample | 2.14 | 0.03 | 2.47 |
|
| dist.template | 11.31 | 0.03 | 11.34 |
|
| flowMatch-package | 22.20 | 0.05 | 22.28 |
|
| mahalanobis.dist | 1.38 | 0.00 | 1.39 |
|
| match.clusters | 14.72 | 0.06 | 14.77 |
|
| symmetric.KL | 1.49 | 0.02 | 1.51 |
|
| template.tree | 24.95 | 0.11 | 25.06 |
|
flowMatch.Rcheck/examples_x64/flowMatch-Ex.timings:
| name | user | system | elapsed
|
| Cluster-class | 1.90 | 0.01 | 1.92 |
|
| ClusterMatch-class | 13.79 | 0.02 | 13.81 |
|
| ClusteredSample-class | 3.01 | 0.03 | 3.04 |
|
| MetaCluster-class | 25.07 | 0.05 | 25.16 |
|
| Template-class | 24.31 | 0.06 | 24.98 |
|
| create.template | 25.36 | 0.03 | 25.55 |
|
| dist.cluster | 1.66 | 0.00 | 1.66 |
|
| dist.matrix | 2.85 | 0.01 | 2.87 |
|
| dist.sample | 3.20 | 0.02 | 3.21 |
|
| dist.template | 10.78 | 0.00 | 10.78 |
|
| flowMatch-package | 22.74 | 0.03 | 22.78 |
|
| mahalanobis.dist | 1.98 | 0.03 | 2.01 |
|
| match.clusters | 14.60 | 0.02 | 15.21 |
|
| symmetric.KL | 1.37 | 0.03 | 1.41 |
|
| template.tree | 22.92 | 0.05 | 22.97 |
|