Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:12 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 732/2251 | 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 | |||||||||
merida1 | 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. |
Package: flowMatch |
Version: 1.39.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMatch_1.39.0.tar.gz |
StartedAt: 2024-03-02 04:08:21 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 04:12:23 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 242.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowMatch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMatch_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 is not available * 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 15.528 0.311 18.852 create.template 15.312 0.343 21.249 MetaCluster-class 13.238 0.253 16.078 template.tree 12.741 0.207 15.564 flowMatch-package 12.108 0.283 14.477 ClusterMatch-class 7.261 0.136 8.382 match.clusters 6.883 0.139 8.498 dist.template 5.100 0.114 5.331 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowMatch.Rcheck/00check.log’ for details.
flowMatch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowMatch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘flowMatch’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BipartiteGraph.cpp -o BipartiteGraph.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MinWghtEdgCoverBipartite.cpp -o MinWghtEdgCoverBipartite.o MinWghtEdgCoverBipartite.cpp:487:10: warning: variable 'delta_cx_cy' set but not used [-Wunused-but-set-variable] int delta_cx_cy = 0; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c flowMatch.cpp -o flowMatch.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o flowMatch.so BipartiteGraph.o MinWghtEdgCoverBipartite.o flowMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 0.843 | 0.067 | 1.042 | |
ClusterMatch-class | 7.261 | 0.136 | 8.382 | |
ClusteredSample-class | 1.905 | 0.399 | 2.756 | |
MetaCluster-class | 13.238 | 0.253 | 16.078 | |
Template-class | 15.528 | 0.311 | 18.852 | |
create.template | 15.312 | 0.343 | 21.249 | |
dist.cluster | 0.672 | 0.029 | 1.068 | |
dist.matrix | 1.315 | 0.046 | 1.418 | |
dist.sample | 1.190 | 0.036 | 1.274 | |
dist.template | 5.100 | 0.114 | 5.331 | |
flowMatch-package | 12.108 | 0.283 | 14.477 | |
mahalanobis.dist | 0.693 | 0.024 | 0.745 | |
match.clusters | 6.883 | 0.139 | 8.498 | |
symmetric.KL | 0.951 | 0.028 | 1.241 | |
template.tree | 12.741 | 0.207 | 15.564 | |