Ariful Azad
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/flowMatch |
| git_branch: devel |
| git_last_commit: 4868960 |
| git_last_commit_date: 2023-10-24 09:56:54 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:43 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 737/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowMatch 1.39.0 (landing page) Ariful Azad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: flowMatch |
| Version: 1.39.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings flowMatch_1.39.0.tar.gz |
| StartedAt: 2024-03-28 05:25:15 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:27:32 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 136.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowMatch.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings flowMatch_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMatch’ version ‘1.39.0’
* 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++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
libs 5.0Mb
* 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 11.627 0.032 11.688
Template-class 11.442 0.047 11.517
flowMatch-package 9.999 0.019 10.045
MetaCluster-class 9.959 0.028 10.007
template.tree 9.547 0.020 9.588
ClusterMatch-class 5.751 0.012 5.776
match.clusters 5.744 0.000 5.755
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck/00check.log’
for details.
flowMatch.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL flowMatch
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘flowMatch’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:271:16: 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++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:43:16: 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++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)
flowMatch.Rcheck/flowMatch-Ex.timings
| name | user | system | elapsed | |
| Cluster-class | 0.601 | 0.048 | 0.666 | |
| ClusterMatch-class | 5.751 | 0.012 | 5.776 | |
| ClusteredSample-class | 1.382 | 0.020 | 1.406 | |
| MetaCluster-class | 9.959 | 0.028 | 10.007 | |
| Template-class | 11.442 | 0.047 | 11.517 | |
| create.template | 11.627 | 0.032 | 11.688 | |
| dist.cluster | 0.608 | 0.000 | 0.610 | |
| dist.matrix | 1.087 | 0.000 | 1.089 | |
| dist.sample | 1.237 | 0.008 | 1.247 | |
| dist.template | 4.633 | 0.004 | 4.649 | |
| flowMatch-package | 9.999 | 0.019 | 10.045 | |
| mahalanobis.dist | 0.624 | 0.004 | 0.629 | |
| match.clusters | 5.744 | 0.000 | 5.755 | |
| symmetric.KL | 0.639 | 0.004 | 0.643 | |
| template.tree | 9.547 | 0.020 | 9.588 | |