| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:29 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 687/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowMatch 1.35.0 (landing page) Ariful Azad
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: flowMatch |
| Version: 1.35.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMatch.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings flowMatch_1.35.0.tar.gz |
| StartedAt: 2022-12-28 23:51:37 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:53:33 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 116.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowMatch.Rcheck |
| Warnings: 0 |
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowMatch.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings flowMatch_1.35.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/flowMatch.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flowMatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowMatch' version '1.35.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 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-3.17-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 nor [v]sprintf. 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
create.template 7.26 0.25 7.51
Template-class 7.19 0.25 7.44
MetaCluster-class 6.14 0.37 6.51
flowMatch-package 6.39 0.09 6.48
template.tree 5.76 0.06 5.83
* 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-3.17-bioc-rtools43/meat/flowMatch.Rcheck/00check.log'
for details.
flowMatch.Rcheck/00install.out
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL flowMatch
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'flowMatch' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-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++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-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:271:23: 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:487:45: 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:804:26: warning: 'template2' may be used uninitialized [-Wmaybe-uninitialized]
804 | rearrange(templatePairs, mergedTemplate, template1, template2,lambda);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MinWghtEdgCoverBipartite.cpp:787:32: note: 'template2' was declared here
787 | int template1, template2;
| ^~~~~~~~~
MinWghtEdgCoverBipartite.cpp:804:26: warning: 'template1' may be used uninitialized [-Wmaybe-uninitialized]
804 | rearrange(templatePairs, mergedTemplate, template1, template2,lambda);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MinWghtEdgCoverBipartite.cpp:787:21: note: 'template1' was declared here
787 | int template1, template2;
| ^~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-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:43:23: 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:45:31: 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:53:23: 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:55:31: 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++11 -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-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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 | 0.44 | 0.07 | 0.57 | |
| ClusterMatch-class | 3.74 | 0.23 | 3.97 | |
| ClusteredSample-class | 0.86 | 0.13 | 0.99 | |
| MetaCluster-class | 6.14 | 0.37 | 6.51 | |
| Template-class | 7.19 | 0.25 | 7.44 | |
| create.template | 7.26 | 0.25 | 7.51 | |
| dist.cluster | 0.42 | 0.03 | 0.46 | |
| dist.matrix | 0.80 | 0.05 | 0.84 | |
| dist.sample | 0.66 | 0.01 | 0.67 | |
| dist.template | 2.67 | 0.08 | 2.75 | |
| flowMatch-package | 6.39 | 0.09 | 6.48 | |
| mahalanobis.dist | 0.39 | 0.02 | 0.41 | |
| match.clusters | 3.42 | 0.07 | 3.49 | |
| symmetric.KL | 0.55 | 0.04 | 0.59 | |
| template.tree | 5.76 | 0.06 | 5.83 | |