Ahmed Mohamed
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/NetPathMiner |
| Branch: master |
| Last Commit: df342e5 |
| Last Changed Date: 2019-10-29 13:37:30 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:38:58 -0500 (Thu, 16 Jan 2020).
| Package 1144/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NetPathMiner 1.23.0 Ahmed Mohamed
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: NetPathMiner |
| Version: 1.23.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NetPathMiner_1.23.0.tar.gz |
| StartedAt: 2020-01-16 06:58:09 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:00:00 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 111.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: NetPathMiner.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NetPathMiner_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/NetPathMiner.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.23.0’
* 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 ... WARNING
Found the following significant warnings:
'config' variable 'CPP' is deprecated
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/NetPathMiner.Rcheck/00install.out’ for details.
* 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 ... 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 ‘.to’
getPaths: no visible global function definition for ‘.from’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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’
vertexDeleteReconnect: no visible global function definition for ‘.nei’
Undefined global functions or variables:
.from .nei .to 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
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",
"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 ... 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 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 15.451 0.097 16.124
plotAllNetworks 12.578 0.092 13.619
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.
NetPathMiner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NetPathMiner ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘NetPathMiner’ ... ** using staged installation 'config' variable 'CPP' is deprecated checking for gcc... clang 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 accepts -g... yes checking for clang option to accept ISO C89... none needed checking how to run the C preprocessor... clang -E checking for xmlParseFile in -lxml2... yes checking for readSBML in -lsbml... no untarring boost include tree... SBML not found. libXML2 found checking for xml2-config... /usr/bin/xml2-config configure: creating ./config.status config.status: creating src/Makevars ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c PathRanker.cpp -o PathRanker.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c handlesegfault.c -o handlesegfault.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c hme3m.c -o hme3m.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c kgml_interface.cpp -o kgml_interface.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c methods.cpp -o methods.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c pathScope.cpp -o pathScope.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I . -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -fPIC -Wall -g -O2 -c sbml_interface.cpp -o sbml_interface.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lxml2 -lxml2 -lz -lpthread -licucore -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/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 | 0.320 | 0.014 | 0.339 | |
| MIRIAM | 0.128 | 0.015 | 0.143 | |
| NPMdefaults | 0.016 | 0.006 | 0.023 | |
| SBML2igraph | 0.001 | 0.001 | 0.002 | |
| assignEdgeWeights | 0.484 | 0.011 | 0.495 | |
| biopax2igraph | 3.058 | 0.535 | 1.118 | |
| colorVertexByAttr | 0.610 | 0.406 | 0.253 | |
| ex_biopax | 0.059 | 0.034 | 0.036 | |
| ex_kgml_sig | 0.688 | 0.435 | 0.323 | |
| ex_microarray | 0.005 | 0.003 | 0.007 | |
| ex_sbml | 1.479 | 0.016 | 1.497 | |
| extractPathNetwork | 1.937 | 0.071 | 2.010 | |
| getAttr | 0.037 | 0.009 | 0.046 | |
| getGeneSetNetworks | 0.012 | 0.003 | 0.015 | |
| getGeneSets | 0.077 | 0.006 | 0.083 | |
| getPathsAsEIDs | 1.481 | 0.044 | 1.525 | |
| layoutVertexByAttr | 0.564 | 0.014 | 0.579 | |
| makeGeneNetwork | 0.176 | 0.005 | 0.182 | |
| makeMetaboliteNetwork | 0.077 | 0.002 | 0.079 | |
| makeReactionNetwork | 0.106 | 0.003 | 0.108 | |
| pathClassifier | 0.817 | 0.068 | 0.889 | |
| pathCluster | 0.420 | 0.014 | 0.492 | |
| pathRanker | 1.046 | 0.050 | 1.096 | |
| pathsToBinary | 0.833 | 0.013 | 0.847 | |
| plotAllNetworks | 12.578 | 0.092 | 13.619 | |
| plotClusters | 1.275 | 0.015 | 1.631 | |
| plotCytoscape | 0.528 | 0.008 | 0.661 | |
| plotNetwork | 0.833 | 0.025 | 0.905 | |
| plotPathClassifier | 0.989 | 0.030 | 1.085 | |
| plotPathCluster | 0.526 | 0.019 | 0.686 | |
| plotPaths | 15.451 | 0.097 | 16.124 | |
| predictPathClassifier | 0.782 | 0.012 | 0.794 | |
| predictPathCluster | 0.370 | 0.007 | 0.400 | |
| reindexNetwork | 0.261 | 0.010 | 0.270 | |
| rmSmallCompounds | 0.120 | 0.004 | 0.123 | |
| samplePaths | 0.833 | 0.025 | 0.859 | |
| simplifyReactionNetwork | 0.187 | 0.004 | 0.190 | |
| toGraphNEL | 1.007 | 0.025 | 1.034 | |
| vertexDeleteReconnect | 0.083 | 0.003 | 0.086 | |