Ariful Azad
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/flowMatch |
| Branch: RELEASE_3_6 |
| Last Commit: 63c9e3c |
| Last Changed Date: 2017-10-30 12:40:10 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:39 -0400 (Thu, 12 Apr 2018).
| Package 483/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowMatch 1.14.0 Ariful Azad
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: flowMatch |
| Version: 1.14.0 |
| Command: rm -rf flowMatch.buildbin-libdir flowMatch.Rcheck && mkdir flowMatch.buildbin-libdir flowMatch.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowMatch.buildbin-libdir flowMatch_1.14.0.tar.gz >flowMatch.Rcheck\00install.out 2>&1 && cp flowMatch.Rcheck\00install.out flowMatch-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowMatch.buildbin-libdir --install="check:flowMatch-install.out" --force-multiarch --no-vignettes --timings flowMatch_1.14.0.tar.gz |
| StartedAt: 2018-04-12 00:01:13 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:06:40 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 327.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowMatch.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf flowMatch.buildbin-libdir flowMatch.Rcheck && mkdir flowMatch.buildbin-libdir flowMatch.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowMatch.buildbin-libdir flowMatch_1.14.0.tar.gz >flowMatch.Rcheck\00install.out 2>&1 && cp flowMatch.Rcheck\00install.out flowMatch-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowMatch.buildbin-libdir --install="check:flowMatch-install.out" --force-multiarch --no-vignettes --timings flowMatch_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowMatch.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.14.0'
* 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 5.7Mb
sub-directories of 1Mb or more:
doc 3.6Mb
libs 1.8Mb
* 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 'C:/Users/biocbuild/bbs-3.6-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 use Fortran I/O
nor system RNGs. 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 15.56 0.06 15.63
flowMatch-package 14.98 0.06 15.05
Template-class 14.91 0.10 15.00
MetaCluster-class 14.85 0.03 14.88
template.tree 13.85 0.08 13.92
ClusterMatch-class 8.66 0.05 8.70
match.clusters 8.36 0.01 8.37
dist.template 6.99 0.03 7.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
create.template 15.48 0.03 15.51
MetaCluster-class 15.30 0.04 15.33
Template-class 15.17 0.01 15.18
flowMatch-package 14.31 0.04 14.36
template.tree 13.56 0.09 13.65
ClusterMatch-class 8.70 0.05 8.75
match.clusters 8.34 0.05 8.39
dist.template 6.72 0.00 6.72
* 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
'C:/Users/biocbuild/bbs-3.6-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"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c BipartiteGraph.cpp -o BipartiteGraph.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -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 -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flowMatch.buildbin-libdir/flowMatch/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'flowMatch'
finding HTML links ... done
Cluster-class html
ClusterMatch-class html
ClusteredSample-class html
MetaCluster-class html
Template-class html
create.template html
dist.cluster html
dist.matrix html
dist.sample html
dist.template html
flowMatch-package html
mahalanobis.dist html
match.clusters html
symmetric.KL html
template.tree html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'flowMatch' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c BipartiteGraph.cpp -o BipartiteGraph.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -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 -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/flowMatch.buildbin-libdir/flowMatch/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowMatch' as flowMatch_1.14.0.zip
* DONE (flowMatch)
In R CMD INSTALL
In R CMD INSTALL
|
flowMatch.Rcheck/examples_i386/flowMatch-Ex.timings
|
flowMatch.Rcheck/examples_x64/flowMatch-Ex.timings
|