Ariful Azad
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/flowMatch |
| git_branch: RELEASE_3_16 |
| git_last_commit: 294abce |
| git_last_commit_date: 2022-11-01 11:09:01 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:33 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 698/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowMatch 1.34.0 (landing page) Ariful Azad
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: flowMatch |
| Version: 1.34.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMatch.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings flowMatch_1.34.0.tar.gz |
| StartedAt: 2023-04-11 01:33:47 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:35:53 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 125.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowMatch.Rcheck |
| Warnings: 0 |
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### Running command:
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### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMatch.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings flowMatch_1.34.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/flowMatch.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.34.0'
* 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 ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/flowMatch/libs/x64/flowMatch.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Template-class 7.69 0.30 7.99
create.template 7.56 0.15 7.73
MetaCluster-class 6.11 0.33 6.43
flowMatch-package 6.02 0.18 6.22
template.tree 5.99 0.08 6.06
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/flowMatch.Rcheck/00check.log'
for details.
flowMatch.Rcheck/00install.out
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### Running command:
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### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL flowMatch
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'flowMatch' ...
** using staged installation
** libs
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BipartiteGraph.cpp -o BipartiteGraph.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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;
| ^~~~~~~~~~~
MinWghtEdgCoverBipartite.cpp: In function 'classTemplate buildTemplate(std::vector<std::vector<templatePair> >&, double, mclust&)':
MinWghtEdgCoverBipartite.cpp:804:12: warning: 'template2' may be used uninitialized in this function [-Wmaybe-uninitialized]
804 | rearrange(templatePairs, mergedTemplate, template1, template2,lambda);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MinWghtEdgCoverBipartite.cpp:804:12: warning: 'template1' may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 long unsigned int'} [-Wsign-compare]
55 | for(int j=0; j<mec.tCoverVecVec[i].size(); j++)
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -s -static-libgcc -o flowMatch.dll tmp.def BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-flowMatch/00new/flowMatch/libs/x64
** 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
** 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 | 0.39 | 0.07 | 0.59 | |
| ClusterMatch-class | 3.66 | 0.20 | 3.86 | |
| ClusteredSample-class | 1.04 | 0.10 | 1.14 | |
| MetaCluster-class | 6.11 | 0.33 | 6.43 | |
| Template-class | 7.69 | 0.30 | 7.99 | |
| create.template | 7.56 | 0.15 | 7.73 | |
| dist.cluster | 0.39 | 0.02 | 0.41 | |
| dist.matrix | 0.67 | 0.06 | 0.73 | |
| dist.sample | 0.72 | 0.02 | 0.73 | |
| dist.template | 2.62 | 0.08 | 2.71 | |
| flowMatch-package | 6.02 | 0.18 | 6.22 | |
| mahalanobis.dist | 0.37 | 0.05 | 0.42 | |
| match.clusters | 3.66 | 0.03 | 3.69 | |
| symmetric.KL | 0.59 | 0.01 | 0.61 | |
| template.tree | 5.99 | 0.08 | 6.06 | |