Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1409/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NetPathMiner 1.42.0 (landing page) Ahmed Mohamed
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the NetPathMiner package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NetPathMiner.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: NetPathMiner |
Version: 1.42.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetPathMiner_1.42.0.tar.gz |
StartedAt: 2024-12-20 06:52:01 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:54:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 127.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NetPathMiner.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetPathMiner_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/NetPathMiner.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘NetPathMiner/DESCRIPTION’ ... OK * this is package ‘NetPathMiner’ version ‘1.42.0’ * package encoding: UTF-8 * 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 ‘NetPathMiner’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE alpha: no visible global function definition for ‘col2rgb’ alpha: no visible global function definition for ‘rgb’ assignEdgeWeights : wt.func: no visible global function definition for ‘median’ assignEdgeWeights: no visible global function definition for ‘complete.cases’ assignEdgeWeights: no visible global function definition for ‘na.omit’ assignEdgeWeights : <anonymous>: no visible global function definition for ‘na.omit’ bpGetAnnFromXRef: no visible global function definition for ‘na.omit’ bpGetReferences: no visible global function definition for ‘setNames’ bpMetabolicL2: no visible global function definition for ‘setNames’ bpMetabolicL3: no visible global function definition for ‘setNames’ bpSignalingL3: no visible global function definition for ‘na.omit’ bpSplitComplex: no visible global function definition for ‘na.omit’ colorVertexByAttr: no visible global function definition for ‘palette’ colorVertexByAttr: no visible global function definition for ‘colorRampPalette’ drawLegend: no visible global function definition for ‘par’ drawLegend: no visible global function definition for ‘plot.new’ drawLegend: no visible global function definition for ‘strwidth’ drawLegend: no visible global function definition for ‘legend’ fetchAttribute: no visible global function definition for ‘na.omit’ fetchAttribute: no visible global function definition for ‘URLencode’ fetchAttribute: no visible global function definition for ‘setNames’ fetchAttribute : <anonymous>: no visible global function definition for ‘read.table’ getGeneSetNetworks: no visible global function definition for ‘setClass’ getGeneSetNetworks: no visible global function definition for ‘representation’ getPaths : <anonymous>: no visible global function definition for ‘head’ getPaths: no visible global function definition for ‘tail’ graph.sizes: no visible global function definition for ‘par’ makeReactionNetwork: no visible global function definition for ‘complete.cases’ pathClassifier: no visible binding for global variable ‘sd’ pathClassifier: no visible global function definition for ‘aggregate’ pathCluster: no visible binding for global variable ‘sd’ pathCluster: no visible global function definition for ‘aggregate’ plotAllNetworks: no visible global function definition for ‘palette’ plotAllNetworks: no visible global function definition for ‘par’ plotAllNetworks: no visible global function definition for ‘colorRampPalette’ plotClassifierROC: no visible global function definition for ‘palette’ plotClassifierROC: no visible global function definition for ‘layout’ plotClassifierROC: no visible global function definition for ‘na.omit’ plotClusterMatrix: no visible global function definition for ‘rainbow’ plotClusterMatrix: no visible global function definition for ‘image’ plotClusterMatrix: no visible global function definition for ‘axis’ plotClusterProbs: no visible global function definition for ‘rainbow’ plotClusterProbs: no visible global function definition for ‘matplot’ plotClusters: no visible global function definition for ‘rainbow’ plotClusters: no visible global function definition for ‘strwidth’ plotClusters: no visible global function definition for ‘layout’ plotClusters: no visible global function definition for ‘par’ plotClusters: no visible global function definition for ‘legend’ plotCytoscapeGML : col2hex: no visible global function definition for ‘rgb’ plotCytoscapeGML : col2hex: no visible global function definition for ‘col2rgb’ plotCytoscapeGML: no visible global function definition for ‘packageVersion’ plotNetwork: no visible global function definition for ‘palette’ plotNetwork: no visible global function definition for ‘par’ plotNetwork_internal: no visible global function definition for ‘palette’ plotNetwork_internal: no visible global function definition for ‘setNames’ plotPathClassifier: no visible global function definition for ‘palette’ plotPathClassifier: no visible global function definition for ‘par’ plotPathClassifier: no visible global function definition for ‘layout’ plotPathClassifier: no visible global function definition for ‘barplot’ plotPathClassifier: no visible global function definition for ‘abline’ plotPathClassifier: no visible global function definition for ‘points’ plotPathClassifier: no visible global function definition for ‘axis’ plotPathClassifier: no visible global function definition for ‘image’ plotPathClassifier: no visible global function definition for ‘cm.colors’ plotPathClassifier: no visible global function definition for ‘mtext’ plotPathClassifier: no visible global function definition for ‘lines’ plotPathCluster: no visible global function definition for ‘par’ plotPathCluster: no visible global function definition for ‘layout’ plotPathCluster: no visible global function definition for ‘barplot’ plotPathCluster: no visible global function definition for ‘abline’ plotPathCluster: no visible global function definition for ‘axis’ plotPathCluster: no visible global function definition for ‘image’ plotPathCluster: no visible global function definition for ‘cm.colors’ plotPathCluster: no visible global function definition for ‘mtext’ plotPathROC: no visible global function definition for ‘palette’ plotPathROC: no visible global function definition for ‘lines’ plotPathROC: no visible global function definition for ‘axis’ plotPathROC: no visible global function definition for ‘mtext’ plotPathROC: no visible global function definition for ‘legend’ plotPaths: no visible global function definition for ‘palette’ plotPaths: no visible global function definition for ‘par’ process.color: no visible global function definition for ‘colorRampPalette’ process.color: no visible global function definition for ‘setNames’ process.layout: no visible global function definition for ‘par’ processNetwork : <anonymous>: no visible global function definition for ‘ecdf’ reindexNetwork: no visible binding for global variable ‘head’ stdAttrNames : <anonymous>: no visible global function definition for ‘head’ stdAttrNames : <anonymous>: no visible global function definition for ‘setNames’ Undefined global functions or variables: URLencode abline aggregate axis barplot cm.colors col2rgb colorRampPalette complete.cases ecdf head image layout legend lines matplot median mtext na.omit packageVersion palette par plot.new points rainbow read.table representation rgb sd setClass setNames strwidth tail Consider adding importFrom("grDevices", "cm.colors", "col2rgb", "colorRampPalette", "palette", "rainbow", "rgb") importFrom("graphics", "abline", "axis", "barplot", "image", "layout", "legend", "lines", "matplot", "mtext", "par", "plot.new", "points", "strwidth") importFrom("methods", "representation", "setClass") importFrom("stats", "aggregate", "complete.cases", "ecdf", "median", "na.omit", "sd", "setNames") importFrom("utils", "URLencode", "head", "packageVersion", "read.table", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) plotClassifierROC.Rd:14: Lost braces 14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs}) | ^ checkRd: (-1) plotClassifierROC.Rd:14-17: Lost braces 14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs}) | ^ checkRd: (-1) plotClassifierROC.Rd:18: Lost braces 18 | item{Bottom}{The likelihood convergence history for the HME3M model. If the parameters | ^ checkRd: (-1) plotClassifierROC.Rd:18-19: Lost braces 18 | item{Bottom}{The likelihood convergence history for the HME3M model. If the parameters | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... 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 plotPaths 13.182 0.090 13.709 plotAllNetworks 9.312 0.071 9.450 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/NetPathMiner.Rcheck/00check.log’ for details.
NetPathMiner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetPathMiner ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘NetPathMiner’ ... ** using staged installation 'config' variable 'CPP' is defunct checking for gcc... clang -arch x86_64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -arch x86_64 -E checking for xmlParseFile in -lxml2... yes checking for readSBML in -lsbml... no SBML not found. libXML2 found checking for xml2-config... /usr/bin/xml2-config configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c handlesegfault.c -o handlesegfault.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hme3m.c -o hme3m.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kgml_interface.cpp -o kgml_interface.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methods.cpp -o methods.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sbml_interface.cpp -o sbml_interface.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 NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -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-NetPathMiner/00new/NetPathMiner/libs ** R ** data ** inst ** 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 (NetPathMiner)
NetPathMiner.Rcheck/NetPathMiner-Ex.timings
name | user | system | elapsed | |
KGML2igraph | 0.632 | 0.026 | 0.668 | |
MIRIAM | 0.330 | 0.035 | 0.370 | |
NPMdefaults | 0.013 | 0.015 | 0.029 | |
SBML2igraph | 0.001 | 0.000 | 0.002 | |
assignEdgeWeights | 0.727 | 0.022 | 0.754 | |
biopax2igraph | 0.852 | 0.037 | 0.877 | |
colorVertexByAttr | 0.289 | 0.010 | 0.301 | |
ex_biopax | 0.032 | 0.007 | 0.039 | |
ex_kgml_sig | 0.389 | 0.014 | 0.405 | |
ex_microarray | 0.004 | 0.003 | 0.008 | |
ex_sbml | 1.791 | 0.015 | 1.821 | |
extractPathNetwork | 3.095 | 0.049 | 3.286 | |
getAttr | 0.080 | 0.016 | 0.097 | |
getGeneSetNetworks | 0.056 | 0.003 | 0.060 | |
getGeneSets | 0.177 | 0.007 | 0.188 | |
getPathsAsEIDs | 3.060 | 0.031 | 3.157 | |
layoutVertexByAttr | 0.680 | 0.021 | 0.705 | |
makeGeneNetwork | 0.418 | 0.007 | 0.426 | |
makeMetaboliteNetwork | 0.190 | 0.003 | 0.193 | |
makeReactionNetwork | 0.281 | 0.003 | 0.285 | |
pathClassifier | 1.849 | 0.081 | 1.936 | |
pathCluster | 0.726 | 0.019 | 0.748 | |
pathRanker | 1.477 | 0.018 | 1.522 | |
pathsToBinary | 1.597 | 0.019 | 1.629 | |
plotAllNetworks | 9.312 | 0.071 | 9.450 | |
plotClusters | 1.851 | 0.028 | 1.908 | |
plotCytoscape | 0.689 | 0.011 | 0.705 | |
plotNetwork | 0.992 | 0.032 | 1.035 | |
plotPathClassifier | 1.917 | 0.033 | 1.969 | |
plotPathCluster | 0.837 | 0.014 | 0.857 | |
plotPaths | 13.182 | 0.090 | 13.709 | |
predictPathClassifier | 1.693 | 0.015 | 1.795 | |
predictPathCluster | 0.745 | 0.012 | 0.899 | |
reindexNetwork | 0.424 | 0.011 | 0.468 | |
rmSmallCompounds | 0.159 | 0.006 | 0.339 | |
simplifyReactionNetwork | 0.314 | 0.007 | 0.451 | |
toGraphNEL | 0.776 | 0.014 | 0.815 | |
vertexDeleteReconnect | 0.150 | 0.005 | 0.155 | |