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This page was generated on 2021-11-26 15:04:51 -0500 (Fri, 26 Nov 2021).

CHECK results for flowMatch on nebbiolo2

To the developers/maintainers of the flowMatch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowMatch.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 664/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMatch 1.30.0  (landing page)
Ariful Azad
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/flowMatch
git_branch: RELEASE_3_14
git_last_commit: 87a457c
git_last_commit_date: 2021-10-26 12:11:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowMatch
Version: 1.30.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowMatch_1.30.0.tar.gz
StartedAt: 2021-11-25 09:27:42 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 09:29:15 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 93.7 seconds
RetCode: 0
Status:   OK  
CheckDir: flowMatch.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowMatch_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/flowMatch.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.30.0’
* 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 ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
create.template   7.840  0.012   7.852
Template-class    7.516  0.039   7.556
flowMatch-package 6.441  0.003   6.445
MetaCluster-class 6.240  0.020   6.261
template.tree     6.227  0.004   6.232
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/flowMatch.Rcheck/00check.log’
for details.



Installation output

flowMatch.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL flowMatch
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘flowMatch’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c BipartiteGraph.cpp -o BipartiteGraph.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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 of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  271 |  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]
  487 |      int delta_cx_cy  = 0;
      |          ^~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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 of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   43 |  for(int i=0; i<mec.sCoverVecVec.size(); i++)
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~
flowMatch.cpp:45:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |   for(int j=0; j<mec.sCoverVecVec[i].size(); j++)
      |                ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
flowMatch.cpp:53:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   53 |  for(int i=0; i<mec.tCoverVecVec.size(); i++)
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~
flowMatch.cpp:55:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   55 |   for(int j=0; j<mec.tCoverVecVec[i].size(); j++)
      |                ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)

Tests output


Example timings

flowMatch.Rcheck/flowMatch-Ex.timings

nameusersystemelapsed
Cluster-class0.4820.0360.518
ClusterMatch-class4.0160.0084.025
ClusteredSample-class1.2300.0311.262
MetaCluster-class6.2400.0206.261
Template-class7.5160.0397.556
create.template7.8400.0127.852
dist.cluster0.4770.0050.481
dist.matrix0.8210.0040.825
dist.sample0.7950.0000.795
dist.template3.1160.0083.124
flowMatch-package6.4410.0036.445
mahalanobis.dist0.4710.0050.475
match.clusters3.9080.0073.914
symmetric.KL0.4580.0000.458
template.tree6.2270.0046.232