Ariful Azad
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/flowMatch |
| Branch: RELEASE_3_10 |
| Last Commit: 4a22be7 |
| Last Changed Date: 2019-10-29 13:08:51 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:08:15 -0400 (Wed, 15 Apr 2020).
| Package 592/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowMatch 1.22.0 Ariful Azad
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: flowMatch |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowMatch_1.22.0.tar.gz |
| StartedAt: 2020-04-15 01:59:21 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:01:20 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 119.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowMatch.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowMatch_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flowMatch.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.22.0’
* 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 ... 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
create.template 12.212 0.020 12.324
Template-class 11.328 0.012 11.386
flowMatch-package 9.820 0.012 9.959
MetaCluster-class 9.316 0.028 9.406
template.tree 9.080 0.016 9.183
ClusterMatch-class 5.484 0.028 5.517
match.clusters 5.400 0.008 5.469
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/flowMatch.Rcheck/00check.log’
for details.
flowMatch.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL flowMatch
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘flowMatch’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c BipartiteGraph.cpp -o BipartiteGraph.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/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:271:16: 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;
^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -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++)
~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flowMatch/00new/flowMatch/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowMatch)
flowMatch.Rcheck/flowMatch-Ex.timings
| name | user | system | elapsed | |
| Cluster-class | 0.704 | 0.008 | 0.790 | |
| ClusterMatch-class | 5.484 | 0.028 | 5.517 | |
| ClusteredSample-class | 1.588 | 0.060 | 1.651 | |
| MetaCluster-class | 9.316 | 0.028 | 9.406 | |
| Template-class | 11.328 | 0.012 | 11.386 | |
| create.template | 12.212 | 0.020 | 12.324 | |
| dist.cluster | 0.668 | 0.004 | 0.719 | |
| dist.matrix | 1.272 | 0.004 | 1.284 | |
| dist.sample | 1.116 | 0.000 | 1.120 | |
| dist.template | 4.592 | 0.000 | 4.642 | |
| flowMatch-package | 9.820 | 0.012 | 9.959 | |
| mahalanobis.dist | 0.660 | 0.008 | 0.673 | |
| match.clusters | 5.400 | 0.008 | 5.469 | |
| symmetric.KL | 0.692 | 0.004 | 0.698 | |
| template.tree | 9.080 | 0.016 | 9.183 | |