Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:27:28 -0400 (Thu, 12 Apr 2018).
Package 811/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Mergeomics 1.6.0 Zeyneb Kurt
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: Mergeomics |
Version: 1.6.0 |
Command: rm -rf Mergeomics.buildbin-libdir Mergeomics.Rcheck && mkdir Mergeomics.buildbin-libdir Mergeomics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Mergeomics.buildbin-libdir Mergeomics_1.6.0.tar.gz >Mergeomics.Rcheck\00install.out 2>&1 && cp Mergeomics.Rcheck\00install.out Mergeomics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Mergeomics.buildbin-libdir --install="check:Mergeomics-install.out" --force-multiarch --no-vignettes --timings Mergeomics_1.6.0.tar.gz |
StartedAt: 2018-04-12 01:13:43 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 01:33:59 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 1216.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Mergeomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Mergeomics.buildbin-libdir Mergeomics.Rcheck && mkdir Mergeomics.buildbin-libdir Mergeomics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Mergeomics.buildbin-libdir Mergeomics_1.6.0.tar.gz >Mergeomics.Rcheck\00install.out 2>&1 && cp Mergeomics.Rcheck\00install.out Mergeomics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Mergeomics.buildbin-libdir --install="check:Mergeomics-install.out" --force-multiarch --no-vignettes --timings Mergeomics_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Mergeomics.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'Mergeomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Mergeomics' version '1.6.0' * 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 'Mergeomics' can be installed ... OK * checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: extdata 7.5Mb * 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 * loading checks for arch 'i386' ** 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 loading without being on the library search path ... OK * loading checks for arch 'x64' ** 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 loading without being on the library search path ... 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 kda.analyze: no visible global function definition for 'p.adjust' kda.analyze.exec: no visible global function definition for 'pnorm' kda.analyze.simulate: no visible global function definition for 'rnorm' kda.prepare: no visible global function definition for 'quantile' kda.prepare: no visible global function definition for 'object.size' kda.prepare.screen: no visible global function definition for 'quantile' kda.prepare.screen: no visible global function definition for 'median' kda.start: no visible global function definition for 'object.size' kda2cytoscape: no visible global function definition for 'write.table' kda2cytoscape.colormap: no visible global function definition for 'rainbow' kda2cytoscape.colormap: no visible global function definition for 'col2rgb' kda2himmeli: no visible global function definition for 'quantile' kda2himmeli: no visible global function definition for 'write.table' kda2himmeli.colormap: no visible global function definition for 'rainbow' kda2himmeli.colormap: no visible global function definition for 'col2rgb' ssea.analyze: no visible global function definition for 'qnorm' ssea.analyze: no visible global function definition for 'approx' ssea.analyze: no visible global function definition for 'pnorm' ssea.analyze.simulate: no visible global function definition for 'quantile' ssea.control: no visible global function definition for 'median' ssea.control: no visible global function definition for 'object.size' ssea.meta: no visible global function definition for 'qnorm' ssea.meta: no visible global function definition for 'quantile' ssea.meta: no visible global function definition for 'pnorm' ssea.meta: no visible global function definition for 'median' ssea.meta: no visible global function definition for 'na.omit' ssea.prepare: no visible global function definition for 'median' ssea.prepare: no visible global function definition for 'object.size' ssea.start: no visible global function definition for 'na.omit' ssea.start: no visible global function definition for 'object.size' ssea.start.configure: no visible global function definition for 'write.table' ssea2kda: no visible global function definition for 'na.omit' ssea2kda.import: no visible global function definition for 'na.omit' tool.aggregate: no visible global function definition for 'na.omit' tool.cluster: no visible global function definition for 'as.dist' tool.cluster: no visible global function definition for 'hclust' tool.fdr.bh: no visible global function definition for 'qnorm' tool.fdr.bh: no visible global function definition for 'p.adjust' tool.fdr.bh: no visible global function definition for 'approx' tool.fdr.empirical: no visible global function definition for 'qnorm' tool.fdr.empirical: no visible global function definition for 'approx' tool.metap: no visible global function definition for 'qnorm' tool.metap: no visible global function definition for 'pnorm' tool.normalize: no visible global function definition for 'sd' tool.normalize: no visible global function definition for 'median' tool.normalize: no visible global function definition for 'optim' tool.normalize: no visible global function definition for 'ks.test' tool.normalize.quality: no visible global function definition for 'sd' tool.normalize.quality: no visible global function definition for 'ks.test' tool.overlap: no visible global function definition for 'phyper' tool.read: no visible global function definition for 'read.delim' tool.read: no visible global function definition for 'na.omit' tool.save: no visible global function definition for 'write.table' tool.unify: no visible global function definition for 'sd' tool.unify: no visible global function definition for 'quantile' tool.unify: no visible global function definition for 'approx' Undefined global functions or variables: approx as.dist col2rgb hclust ks.test median na.omit object.size optim p.adjust phyper pnorm qnorm quantile rainbow read.delim rnorm sd write.table Consider adding importFrom("grDevices", "col2rgb", "rainbow") importFrom("stats", "approx", "as.dist", "hclust", "ks.test", "median", "na.omit", "optim", "p.adjust", "phyper", "pnorm", "qnorm", "quantile", "rnorm", "sd") importFrom("utils", "object.size", "read.delim", "write.table") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed ssea.meta 16.74 0.08 16.81 kda.analyze.exec 9.97 0.28 10.25 ssea2kda 9.95 0.03 9.99 kda.analyze.simulate 8.33 0.00 8.33 kda.prepare 8.25 0.00 8.25 kda.analyze.test 8.19 0.04 8.24 ssea2kda.analyze 7.60 0.00 7.59 ssea.finish.genes 5.97 0.00 5.97 ssea2kda.import 5.68 0.01 5.70 ssea.prepare.counts 5.64 0.03 5.67 ssea.finish 5.00 0.03 5.03 ssea.finish.fdr 5.01 0.00 5.01 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed ssea.meta 16.69 0.03 16.72 kda.analyze.test 14.68 0.08 14.76 kda.analyze.exec 14.41 0.04 14.46 kda.analyze.simulate 10.24 0.02 10.25 kda.prepare 10.14 0.03 10.18 ssea2kda 8.53 0.02 8.61 ssea2kda.analyze 8.22 0.02 8.24 ssea.analyze 6.38 0.00 6.38 ssea2kda.import 6.34 0.01 6.36 ssea.analyze.simulate 6.03 0.01 6.05 ssea.finish 5.93 0.00 5.96 ssea.finish.details 5.61 0.03 5.64 ssea.finish.genes 5.42 0.02 5.43 ssea.finish.fdr 5.30 0.03 5.33 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' OK * 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Mergeomics.Rcheck/00check.log' for details.
Mergeomics.Rcheck/00install.out
install for i386 * installing *source* package 'Mergeomics' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'Mergeomics' finding HTML links ... done MSEA.KDA.onestep html Mergeomics-package html job.kda html kda.analyze html kda.analyze.exec html kda.analyze.simulate html kda.analyze.test html kda.configure html kda.finish html kda.finish.estimate html kda.finish.save html kda.finish.summarize html kda.finish.trim html kda.prepare html kda.prepare.overlap html kda.prepare.screen html kda.start html kda.start.edges html kda.start.identify html kda.start.modules html kda2cytoscape html kda2cytoscape.colorize html kda2cytoscape.colormap html kda2cytoscape.drivers html kda2cytoscape.edges html kda2cytoscape.exec html kda2cytoscape.identify html kda2himmeli html kda2himmeli.colorize html kda2himmeli.colormap html kda2himmeli.drivers html kda2himmeli.edges html kda2himmeli.exec html kda2himmeli.identify html ssea.analyze html ssea.analyze.observe html ssea.analyze.randgenes html ssea.analyze.randloci html ssea.analyze.simulate html ssea.analyze.statistic html ssea.control html ssea.finish html ssea.finish.details html ssea.finish.fdr html ssea.finish.genes html ssea.meta html ssea.prepare html ssea.prepare.counts html ssea.prepare.structure html ssea.start html ssea.start.configure html ssea.start.identify html ssea.start.relabel html ssea2kda html ssea2kda.analyze html ssea2kda.import html tool.aggregate html tool.cluster html tool.cluster.static html tool.coalesce html tool.coalesce.exec html tool.coalesce.find html tool.coalesce.merge html tool.fdr html tool.fdr.bh html tool.fdr.empirical html tool.graph html tool.graph.degree html tool.graph.list html tool.metap html tool.normalize html tool.normalize.quality html tool.overlap html tool.read html tool.save html tool.subgraph html tool.subgraph.find html tool.subgraph.search html tool.subgraph.stats html tool.translate html tool.unify html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'Mergeomics' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'Mergeomics' as Mergeomics_1.6.0.zip * DONE (Mergeomics) In R CMD INSTALL In R CMD INSTALL
Mergeomics.Rcheck/tests_i386/runTests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("Mergeomics") KDA Version:12.7.2015 Parameters: Search depth: 1 Search direction: 1 Maximum overlap: 0.33 Minimum module size: 20 Minimum degree: automatic Maximum degree: automatic Edge factor: 0 Random seed: 1 Importing edges... TAIL HEAD WEIGHT Length:140663 Length:140663 Min. :1 Class :character Class :character 1st Qu.:1 Mode :character Mode :character Median :1 Mean :1 3rd Qu.:1 Max. :1 Importing modules... MODULE NODE Length:1643 Length:1643 Class :character Class :character Mode :character Mode :character Graph: 6.143738 Mb Minimum degree set to 20 Maximum degree set to 278 Collecting hubs... 4876 hubs (25.21%) Graph: 9.614761 Mb Analyzing network... 6675: Dhcr7, n=114, p=1.09e-15 6648: Brap, n=20, p=5.50e-01 6643: Usp38, n=23, p=4.72e-07 5582: Yes1, n=319, p=3.53e-03 4746: Tcf7l2, n=73, p=1.57e-02 4708: Tpte, n=86, p=9.49e-02 4511: Plg, n=160, p=1.45e-01 4464: Tsc22d3, n=487, p=7.03e-13 4407: Dntt, n=93, p=9.53e-21 4360: Slc10a6, n=132, p=3.28e-08 4588,..: Lrg1, n=86, p=1.17e-09 MSEA Version:01.04.2016 Parameters: Permutation type: gene Permutations: 100 Random seed: 1 Minimum gene count: 10 Maximum gene count: 500 Maximum overlap between genes: 0.33 Importing modules... MODULE DESCR Length:20 Length:20 Class :character Class :character Mode :character Mode :character MODULE GENE Length:2906 Length:2906 Class :character Class :character Mode :character Mode :character Importing marker values... MARKER VALUE Length:76866 Min. : 0.8094 Class :character 1st Qu.: 0.9450 Mode :character Median : 1.1374 Mean : 1.3944 3rd Qu.: 1.4688 Max. :323.0100 Importing mapping data... GENE MARKER Length:132705 Length:132705 Class :character Class :character Mode :character Mode :character Merging genes containing shared markers... WARNING! Limited overlap analysis due to large number of groups. 119935/1673535 237061/1673535 354008/1673535 477545/1673535 607376/1673535 735698/1673535 866928/1673535 997673/1673535 1133638/1673535 1264044/1673535 1395593/1673535 1528758/1673535 1658337/1673535 1673535 comparisons 21115 comparisons 13861 comparisons 12880 comparisons Job: 7.863396 Mb Preparing data structures... Job: 12.72742 Mb Adding positive controls... Job: 12.96779 Mb Estimating enrichment... 100/100 cycles Normalizing scores... RUNIT TEST PROTOCOL -- Thu Apr 12 01:26:03 2018 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : Mergeomics RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 373.15 1.01 374.20 |
Mergeomics.Rcheck/tests_x64/runTests.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("Mergeomics") KDA Version:12.7.2015 Parameters: Search depth: 1 Search direction: 1 Maximum overlap: 0.33 Minimum module size: 20 Minimum degree: automatic Maximum degree: automatic Edge factor: 0 Random seed: 1 Importing edges... TAIL HEAD WEIGHT Length:140663 Length:140663 Min. :1 Class :character Class :character 1st Qu.:1 Mode :character Mode :character Median :1 Mean :1 3rd Qu.:1 Max. :1 Importing modules... MODULE NODE Length:1643 Length:1643 Class :character Class :character Mode :character Mode :character Graph: 7.251717 Mb Minimum degree set to 20 Maximum degree set to 278 Collecting hubs... 4876 hubs (25.21%) Graph: 12.46993 Mb Analyzing network... 6675: Dhcr7, n=114, p=1.09e-15 6648: Brap, n=20, p=5.50e-01 6643: Usp38, n=23, p=4.72e-07 5582: Yes1, n=319, p=3.53e-03 4746: Tcf7l2, n=73, p=1.57e-02 4708: Tpte, n=86, p=9.49e-02 4511: Plg, n=160, p=1.45e-01 4464: Tsc22d3, n=487, p=7.03e-13 4407: Dntt, n=93, p=9.53e-21 4360: Slc10a6, n=132, p=3.28e-08 4588,..: Lrg1, n=86, p=1.17e-09 MSEA Version:01.04.2016 Parameters: Permutation type: gene Permutations: 100 Random seed: 1 Minimum gene count: 10 Maximum gene count: 500 Maximum overlap between genes: 0.33 Importing modules... MODULE DESCR Length:20 Length:20 Class :character Class :character Mode :character Mode :character MODULE GENE Length:2906 Length:2906 Class :character Class :character Mode :character Mode :character Importing marker values... MARKER VALUE Length:76866 Min. : 0.8094 Class :character 1st Qu.: 0.9450 Mode :character Median : 1.1374 Mean : 1.3944 3rd Qu.: 1.4688 Max. :323.0100 Importing mapping data... GENE MARKER Length:132705 Length:132705 Class :character Class :character Mode :character Mode :character Merging genes containing shared markers... WARNING! Limited overlap analysis due to large number of groups. 95024/1673535 192041/1673535 286047/1673535 379378/1673535 469120/1673535 551480/1673535 628853/1673535 720446/1673535 797356/1673535 864915/1673535 957409/1673535 1044161/1673535 1130495/1673535 1222182/1673535 1318892/1673535 1417357/1673535 1514926/1673535 1579690/1673535 1657421/1673535 1673535 comparisons 21115 comparisons 13861 comparisons 12880 comparisons Job: 10.5818 Mb Preparing data structures... Job: 15.8636 Mb Adding positive controls... Job: 16.14844 Mb Estimating enrichment... 100/100 cycles Normalizing scores... RUNIT TEST PROTOCOL -- Thu Apr 12 01:33:53 2018 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : Mergeomics RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 468.89 0.51 469.39 |
Mergeomics.Rcheck/examples_i386/Mergeomics-Ex.timings
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Mergeomics.Rcheck/examples_x64/Mergeomics-Ex.timings
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