Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 736/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowMatch 1.42.0 (landing page) Ariful Azad
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | 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. |
Package: flowMatch |
Version: 1.42.0 |
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_1.42.0.tar.gz |
StartedAt: 2024-11-19 22:09:06 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 22:14:19 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 313.5 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_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowMatch.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowMatch/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowMatch’ version ‘1.42.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 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 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 6.852 0.223 7.107 Template-class 6.747 0.203 6.972 MetaCluster-class 5.632 0.148 5.797 flowMatch-package 5.522 0.165 5.693 template.tree 5.051 0.111 5.167 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-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 | 0.400 | 0.030 | 0.433 | |
ClusterMatch-class | 3.281 | 0.084 | 3.378 | |
ClusteredSample-class | 0.850 | 0.134 | 0.988 | |
MetaCluster-class | 5.632 | 0.148 | 5.797 | |
Template-class | 6.747 | 0.203 | 6.972 | |
create.template | 6.852 | 0.223 | 7.107 | |
dist.cluster | 0.394 | 0.018 | 0.416 | |
dist.matrix | 0.764 | 0.036 | 0.806 | |
dist.sample | 0.594 | 0.014 | 0.609 | |
dist.template | 2.445 | 0.064 | 2.513 | |
flowMatch-package | 5.522 | 0.165 | 5.693 | |
mahalanobis.dist | 0.334 | 0.008 | 0.343 | |
match.clusters | 2.900 | 0.068 | 2.971 | |
symmetric.KL | 0.317 | 0.005 | 0.324 | |
template.tree | 5.051 | 0.111 | 5.167 | |