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This page was generated on 2019-04-16 11:51:51 -0400 (Tue, 16 Apr 2019).
Package 909/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Mergeomics 1.10.0 Zeyneb Kurt
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: Mergeomics |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Mergeomics_1.10.0.tar.gz |
StartedAt: 2019-04-16 01:13:46 -0400 (Tue, 16 Apr 2019) |
EndedAt: 2019-04-16 01:24:18 -0400 (Tue, 16 Apr 2019) |
EllapsedTime: 632.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Mergeomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Mergeomics_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Mergeomics.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Mergeomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Mergeomics’ version ‘1.10.0’ * 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 ‘Mergeomics’ can be installed ... OK * checking installed package size ... NOTE installed size is 8.4Mb 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 * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed ssea.meta 17.300 0.044 17.361 kda.analyze.exec 11.804 0.044 11.877 kda.analyze.test 10.852 0.008 10.873 kda.prepare 9.520 0.000 9.532 kda.analyze.simulate 9.384 0.016 9.410 ssea2kda 7.080 0.020 7.121 ssea2kda.analyze 6.708 0.008 6.723 ssea2kda.import 6.436 0.008 6.473 ssea.finish.details 6.088 0.000 6.102 ssea.analyze 5.664 0.000 5.702 ssea.finish 4.992 0.016 5.015 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 ‘/home/biocbuild/bbs-3.8-bioc/meat/Mergeomics.Rcheck/00check.log’ for details.
Mergeomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Mergeomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘Mergeomics’ ... ** 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 * DONE (Mergeomics)
Mergeomics.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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: 7.694687 Mb Minimum degree set to 20 Maximum degree set to 278 Collecting hubs... 4876 hubs (25.21%) Graph: 13.28496 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. 131693/1673535 247134/1673535 367275/1673535 502029/1673535 621908/1673535 745041/1673535 853174/1673535 989228/1673535 1125619/1673535 1275907/1673535 1389717/1673535 1496927/1673535 1607136/1673535 1673535 comparisons 21115 comparisons 13861 comparisons 12880 comparisons Job: 11.66891 Mb Preparing data structures... Job: 17.11776 Mb Adding positive controls... Job: 17.42039 Mb Estimating enrichment... 100/100 cycles Normalizing scores... RUNIT TEST PROTOCOL -- Tue Apr 16 01:24:11 2019 *********************************************** 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 452.420 0.456 454.917
Mergeomics.Rcheck/Mergeomics-Ex.timings
name | user | system | elapsed | |
MSEA.KDA.onestep | 0.000 | 0.000 | 0.002 | |
job.kda | 0.016 | 0.000 | 0.018 | |
kda.analyze | 0.020 | 0.000 | 0.045 | |
kda.analyze.exec | 11.804 | 0.044 | 11.877 | |
kda.analyze.simulate | 9.384 | 0.016 | 9.410 | |
kda.analyze.test | 10.852 | 0.008 | 10.873 | |
kda.configure | 0.000 | 0.000 | 0.001 | |
kda.finish | 0.120 | 0.004 | 0.125 | |
kda.finish.estimate | 0.080 | 0.000 | 0.082 | |
kda.finish.save | 0.076 | 0.000 | 0.080 | |
kda.finish.summarize | 0.076 | 0.008 | 0.087 | |
kda.finish.trim | 0.092 | 0.000 | 0.091 | |
kda.prepare | 9.520 | 0.000 | 9.532 | |
kda.prepare.overlap | 0 | 0 | 0 | |
kda.prepare.screen | 0 | 0 | 0 | |
kda.start | 1.120 | 0.000 | 1.123 | |
kda.start.edges | 0.004 | 0.000 | 0.001 | |
kda.start.identify | 0.004 | 0.000 | 0.004 | |
kda.start.modules | 0.004 | 0.000 | 0.001 | |
kda2cytoscape | 0.336 | 0.000 | 0.338 | |
kda2cytoscape.colorize | 0 | 0 | 0 | |
kda2cytoscape.colormap | 0.000 | 0.000 | 0.001 | |
kda2cytoscape.drivers | 0.124 | 0.000 | 0.125 | |
kda2cytoscape.edges | 0.120 | 0.004 | 0.125 | |
kda2cytoscape.exec | 0.156 | 0.000 | 0.154 | |
kda2cytoscape.identify | 0.004 | 0.000 | 0.003 | |
kda2himmeli | 0.432 | 0.000 | 0.442 | |
kda2himmeli.colorize | 0 | 0 | 0 | |
kda2himmeli.colormap | 0.000 | 0.000 | 0.001 | |
kda2himmeli.drivers | 0.144 | 0.004 | 0.147 | |
kda2himmeli.edges | 0.136 | 0.004 | 0.137 | |
kda2himmeli.exec | 0.256 | 0.004 | 0.262 | |
kda2himmeli.identify | 0.004 | 0.000 | 0.003 | |
ssea.analyze | 5.664 | 0.000 | 5.702 | |
ssea.analyze.observe | 3.008 | 0.004 | 3.015 | |
ssea.analyze.randgenes | 2.924 | 0.004 | 2.929 | |
ssea.analyze.randloci | 4.252 | 0.008 | 4.263 | |
ssea.analyze.simulate | 4.600 | 0.008 | 4.613 | |
ssea.analyze.statistic | 0.000 | 0.000 | 0.001 | |
ssea.control | 3.220 | 0.000 | 3.219 | |
ssea.finish | 4.992 | 0.016 | 5.015 | |
ssea.finish.details | 6.088 | 0.000 | 6.102 | |
ssea.finish.fdr | 4.656 | 0.016 | 4.683 | |
ssea.finish.genes | 4.876 | 0.016 | 4.894 | |
ssea.meta | 17.300 | 0.044 | 17.361 | |
ssea.prepare | 2.952 | 0.000 | 2.954 | |
ssea.prepare.counts | 2.728 | 0.000 | 2.728 | |
ssea.prepare.structure | 3.500 | 0.012 | 3.521 | |
ssea.start | 3.824 | 0.004 | 3.830 | |
ssea.start.configure | 0.316 | 0.000 | 0.316 | |
ssea.start.identify | 0.004 | 0.000 | 0.003 | |
ssea.start.relabel | 2.960 | 0.004 | 2.966 | |
ssea2kda | 7.080 | 0.020 | 7.121 | |
ssea2kda.analyze | 6.708 | 0.008 | 6.723 | |
ssea2kda.import | 6.436 | 0.008 | 6.473 | |
tool.aggregate | 0.000 | 0.000 | 0.002 | |
tool.cluster | 0.044 | 0.000 | 0.044 | |
tool.cluster.static | 0.004 | 0.000 | 0.001 | |
tool.coalesce | 0.044 | 0.000 | 0.044 | |
tool.coalesce.exec | 0.104 | 0.000 | 0.106 | |
tool.coalesce.find | 0.108 | 0.000 | 0.109 | |
tool.coalesce.merge | 0.112 | 0.000 | 0.112 | |
tool.fdr | 0.000 | 0.000 | 0.001 | |
tool.fdr.bh | 0.000 | 0.000 | 0.001 | |
tool.fdr.empirical | 0.000 | 0.000 | 0.001 | |
tool.graph | 1.136 | 0.008 | 1.146 | |
tool.graph.degree | 1.440 | 0.020 | 1.461 | |
tool.graph.list | 1.272 | 0.000 | 1.271 | |
tool.metap | 0.004 | 0.000 | 0.004 | |
tool.normalize | 0.012 | 0.000 | 0.014 | |
tool.normalize.quality | 0.012 | 0.000 | 0.011 | |
tool.overlap | 0.008 | 0.000 | 0.007 | |
tool.read | 0.196 | 0.004 | 0.200 | |
tool.save | 0.004 | 0.000 | 0.001 | |
tool.subgraph | 0.088 | 0.000 | 0.089 | |
tool.subgraph.find | 0.088 | 0.000 | 0.086 | |
tool.subgraph.search | 0.088 | 0.004 | 0.094 | |
tool.subgraph.stats | 0.096 | 0.000 | 0.097 | |
tool.translate | 0.044 | 0.000 | 0.043 | |
tool.unify | 0.000 | 0.000 | 0.002 | |