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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 744/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMatch 1.40.0  (landing page)
Ariful Azad
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/flowMatch
git_branch: RELEASE_3_19
git_last_commit: e80de10
git_last_commit_date: 2024-04-30 10:34:30 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for flowMatch on nebbiolo1

To the developers/maintainers of the flowMatch package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: flowMatch
Version: 1.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowMatch_1.40.0.tar.gz
StartedAt: 2024-06-09 23:05:48 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:07:46 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 117.3 seconds
RetCode: 0
Status:   OK  
CheckDir: flowMatch.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowMatch_1.40.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.40.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 code 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 ... 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 ... NOTE
checkRd: (-1) ClusteredSample-class.Rd:32: Lost braces
    32 |     \item{\code{labels } {A vector of integers (from \code{1:num.clusters}) indicating the cluster to which each point is allocated. This is usually obtained from a clustering algorithm.}}
       |                          ^
checkRd: (-1) ClusteredSample-class.Rd:33: Lost braces
    33 |     \item{\code{centers } {A list of length \code{num.clusters} storing the centers of the clusters. The ith entry of the list \code{centers[[i]]} stores the center of the ith cluster. If not specified, the constructor estimates \code{centers} from \code{sample}.}}
       |                           ^
checkRd: (-1) ClusteredSample-class.Rd:34: Lost braces
    34 |     \item{\code{covs }  {A list of length \code{num.clusters} storing the covariance matrices of the clusters. The ith entry of the list \code{cov[[i]]} stores the covariance matrix of the ith cluster. If not specified, the constructor estimates \code{cov} from \code{sample}.}}
       |                         ^
checkRd: (-1) ClusteredSample-class.Rd:35: Lost braces
    35 |     \item \code{sample } {A matrix, data frame of observations, or object of class \code{flowFrame}.  Rows correspond to observations and columns correspond to variables. It must be passed to the constructor if either \code{centers} or \code{cov} is unspecified; then \code{centers} or  \code{cov} is estimated from \code{sample}.}    
       |                          ^
checkRd: (-1) ClusteredSample-class.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClusteredSample-class.Rd:95: Lost braces
    95 |       \item{\code{sample: } {A matrix, data.frame or an object of class  \code{flowFrame} representing an FC sample.}}
       |                             ^
checkRd: (-1) ClusteredSample-class.Rd:96: Lost braces
    96 |       \item{\code{ClusteredSample: } { An object of class \code{ClusteredSample} storing the clustering of the sample.}}
       |                                      ^
checkRd: (-1) ClusteredSample-class.Rd:97: Lost braces; missing escapes or markup?
    97 |       \item{\code{... } {Other usual plotting related parameters.}} 
       |                         ^
checkRd: (-1) MetaCluster-class.Rd:87: Lost braces
    87 |       \item{\code{mc } {An object of class  \code{MetaCluster} for which the plot function is invoked.}}
       |                        ^
checkRd: (-1) MetaCluster-class.Rd:88: Lost braces; missing escapes or markup?
    88 |       \item{\code{alpha } { (1-alpha)*100\% quantile of the distribution of the clusters or meta-cluster is plotted.}}
       |                           ^
checkRd: (-1) MetaCluster-class.Rd:89: Lost braces; missing escapes or markup?
    89 |       \item{\code{plot.mc }  { TRUE/FALSE, when TRUE the functions draws contour of the combined meta-cluster and when FALSE the function draws the contours of the individual clusters.}}
       |                              ^
checkRd: (-1) MetaCluster-class.Rd:90: Lost braces; missing escapes or markup?
    90 |       \item{\code{... } {Other usual plotting related parameters.}} 
       |                         ^
checkRd: (-1) Template-class.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Template-class.Rd:101: Lost braces in \itemize; meant \describe ?
* 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   8.516  0.040   8.557
Template-class    8.332  0.048   8.380
flowMatch-package 6.974  0.023   6.999
MetaCluster-class 6.869  0.024   6.892
template.tree     6.523  0.016   6.539
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck/00check.log’
for details.


Installation output

flowMatch.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL flowMatch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘flowMatch’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c BipartiteGraph.cpp -o BipartiteGraph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-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:271:23: 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:487:45: warning: variable ‘delta_cx_cy’ set but not used [-Wunused-but-set-variable]
  487 |                                         int delta_cx_cy  = 0;
      |                                             ^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-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:43:23: 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:45:31: 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:53:23: 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:55:31: 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++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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-class0.5060.0150.524
ClusterMatch-class4.0500.1914.243
ClusteredSample-class1.2230.1561.379
MetaCluster-class6.8690.0246.892
Template-class8.3320.0488.380
create.template8.5160.0408.557
dist.cluster0.4860.0040.489
dist.matrix0.9310.0070.939
dist.sample0.7560.0110.767
dist.template3.1370.0083.144
flowMatch-package6.9740.0236.999
mahalanobis.dist0.4700.0120.482
match.clusters4.0580.0044.061
symmetric.KL0.4630.0080.472
template.tree6.5230.0166.539