Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:42 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 1200/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Mergeomics 1.32.0 (landing page) Zeyneb Kurt
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the Mergeomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Mergeomics.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: Mergeomics |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.32.0.tar.gz |
StartedAt: 2024-07-08 07:14:11 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 07:35:57 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 1305.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Mergeomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Mergeomics.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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Mergeomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Mergeomics’ version ‘1.32.0’ * 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 8.3Mb 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 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 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 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 kda.analyze.exec 19.090 0.420 23.228 kda.prepare 18.514 0.289 22.414 kda.analyze.simulate 18.436 0.307 21.666 kda.analyze.test 18.226 0.304 22.482 ssea2kda 12.397 0.274 15.053 ssea2kda.analyze 12.109 0.255 15.573 ssea.meta 10.428 0.218 13.258 ssea2kda.import 10.285 0.194 12.300 ssea.finish.details 9.941 0.221 11.996 ssea.analyze 9.653 0.271 12.092 ssea.finish.genes 9.733 0.165 11.285 ssea.finish 9.690 0.199 11.925 ssea.finish.fdr 9.509 0.174 11.311 ssea.analyze.simulate 9.172 0.205 11.316 ssea.prepare 7.738 0.093 10.106 ssea.analyze.randgenes 7.690 0.107 9.129 ssea.analyze.randloci 7.563 0.111 8.979 ssea.analyze.observe 7.501 0.109 9.393 ssea.control 7.403 0.103 8.951 ssea.prepare.structure 7.237 0.086 10.041 ssea.prepare.counts 7.217 0.089 9.508 ssea.start.relabel 7.165 0.091 8.535 ssea.start 6.964 0.084 8.216 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/Mergeomics.Rcheck/00check.log’ for details.
Mergeomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Mergeomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Mergeomics’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Mergeomics)
Mergeomics.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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... 3741 hubs (15062 nodes) 4876 hubs (25.21%) Graph: 13.28768 Mb Analyzing network... 6675: Dhcr7, n=114, p=2.24e-17 6648: Cit, n=20, p=7.89e-01 6643: Pbx4, n=23, p=2.32e-05 5582: Sypl, n=319, p=2.02e-02 4746: Tcf7l2, n=73, p=2.63e-02 4708: Tpte, n=86, p=5.05e-02 4511: Pzp, n=160, p=8.85e-03 4464: Tsc22d3, n=487, p=4.28e-13 4407: Dntt, n=93, p=2.40e-20 4360: Amica1, n=132, p=1.06e-06 4588,..: Lrg1, n=86, p=5.76e-12 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. 48137/1673535 99710/1673535 146754/1673535 199452/1673535 252483/1673535 305876/1673535 360447/1673535 413726/1673535 467042/1673535 520098/1673535 571547/1673535 622548/1673535 674636/1673535 726271/1673535 778438/1673535 829305/1673535 881895/1673535 933081/1673535 984367/1673535 1035521/1673535 1087065/1673535 1138608/1673535 1189914/1673535 1240816/1673535 1292268/1673535 1343822/1673535 1394473/1673535 1446282/1673535 1498548/1673535 1550109/1673535 1601271/1673535 1652375/1673535 1673535 comparisons 21115 comparisons 13861 comparisons 12880 comparisons Job: 11.66892 Mb Preparing data structures... Job: 17.11777 Mb Adding positive controls... Job: 17.42039 Mb Estimating enrichment... 100/100 cycles Normalizing scores... RUNIT TEST PROTOCOL -- Mon Jul 8 07:35:29 2024 *********************************************** 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 726.680 15.472 876.038
Mergeomics.Rcheck/Mergeomics-Ex.timings
name | user | system | elapsed | |
MSEA.KDA.onestep | 0.005 | 0.003 | 0.011 | |
job.kda | 0.029 | 0.007 | 0.065 | |
kda.analyze | 0.017 | 0.006 | 0.029 | |
kda.analyze.exec | 19.090 | 0.420 | 23.228 | |
kda.analyze.simulate | 18.436 | 0.307 | 21.666 | |
kda.analyze.test | 18.226 | 0.304 | 22.482 | |
kda.configure | 0.001 | 0.001 | 0.003 | |
kda.finish | 0.236 | 0.017 | 0.340 | |
kda.finish.estimate | 0.142 | 0.005 | 0.173 | |
kda.finish.save | 0.143 | 0.005 | 0.178 | |
kda.finish.summarize | 0.142 | 0.004 | 0.171 | |
kda.finish.trim | 0.142 | 0.004 | 0.170 | |
kda.prepare | 18.514 | 0.289 | 22.414 | |
kda.prepare.overlap | 0.000 | 0.003 | 0.003 | |
kda.prepare.screen | 0.000 | 0.001 | 0.002 | |
kda.start | 2.524 | 0.078 | 3.240 | |
kda.start.edges | 0.003 | 0.002 | 0.008 | |
kda.start.identify | 0.010 | 0.002 | 0.011 | |
kda.start.modules | 0.003 | 0.002 | 0.006 | |
kda2cytoscape | 0.727 | 0.021 | 0.912 | |
kda2cytoscape.colorize | 0.001 | 0.001 | 0.001 | |
kda2cytoscape.colormap | 0.000 | 0.000 | 0.002 | |
kda2cytoscape.drivers | 0.246 | 0.013 | 0.311 | |
kda2cytoscape.edges | 0.237 | 0.013 | 0.286 | |
kda2cytoscape.exec | 0.290 | 0.014 | 0.353 | |
kda2cytoscape.identify | 0.008 | 0.002 | 0.009 | |
kda2himmeli | 0.747 | 0.025 | 0.919 | |
kda2himmeli.colorize | 0.001 | 0.001 | 0.001 | |
kda2himmeli.colormap | 0.001 | 0.000 | 0.001 | |
kda2himmeli.drivers | 0.245 | 0.014 | 0.321 | |
kda2himmeli.edges | 0.248 | 0.014 | 0.305 | |
kda2himmeli.exec | 0.452 | 0.023 | 0.576 | |
kda2himmeli.identify | 0.008 | 0.001 | 0.011 | |
ssea.analyze | 9.653 | 0.271 | 12.092 | |
ssea.analyze.observe | 7.501 | 0.109 | 9.393 | |
ssea.analyze.randgenes | 7.690 | 0.107 | 9.129 | |
ssea.analyze.randloci | 7.563 | 0.111 | 8.979 | |
ssea.analyze.simulate | 9.172 | 0.205 | 11.316 | |
ssea.analyze.statistic | 0.001 | 0.001 | 0.002 | |
ssea.control | 7.403 | 0.103 | 8.951 | |
ssea.finish | 9.690 | 0.199 | 11.925 | |
ssea.finish.details | 9.941 | 0.221 | 11.996 | |
ssea.finish.fdr | 9.509 | 0.174 | 11.311 | |
ssea.finish.genes | 9.733 | 0.165 | 11.285 | |
ssea.meta | 10.428 | 0.218 | 13.258 | |
ssea.prepare | 7.738 | 0.093 | 10.106 | |
ssea.prepare.counts | 7.217 | 0.089 | 9.508 | |
ssea.prepare.structure | 7.237 | 0.086 | 10.041 | |
ssea.start | 6.964 | 0.084 | 8.216 | |
ssea.start.configure | 0.608 | 0.032 | 0.793 | |
ssea.start.identify | 0.010 | 0.002 | 0.015 | |
ssea.start.relabel | 7.165 | 0.091 | 8.535 | |
ssea2kda | 12.397 | 0.274 | 15.053 | |
ssea2kda.analyze | 12.109 | 0.255 | 15.573 | |
ssea2kda.import | 10.285 | 0.194 | 12.300 | |
tool.aggregate | 0.003 | 0.002 | 0.007 | |
tool.cluster | 0.034 | 0.002 | 0.047 | |
tool.cluster.static | 0.002 | 0.001 | 0.003 | |
tool.coalesce | 0.087 | 0.003 | 0.111 | |
tool.coalesce.exec | 0.276 | 0.004 | 0.317 | |
tool.coalesce.find | 0.265 | 0.004 | 0.304 | |
tool.coalesce.merge | 0.264 | 0.003 | 0.313 | |
tool.fdr | 0.002 | 0.001 | 0.002 | |
tool.fdr.bh | 0.001 | 0.001 | 0.001 | |
tool.fdr.empirical | 0.001 | 0.000 | 0.004 | |
tool.graph | 2.374 | 0.057 | 2.833 | |
tool.graph.degree | 2.666 | 0.078 | 3.226 | |
tool.graph.list | 2.420 | 0.060 | 2.895 | |
tool.metap | 0.006 | 0.002 | 0.009 | |
tool.normalize | 0.045 | 0.004 | 0.058 | |
tool.normalize.quality | 0.025 | 0.002 | 0.031 | |
tool.overlap | 0.014 | 0.002 | 0.018 | |
tool.read | 0.388 | 0.013 | 0.548 | |
tool.save | 0.002 | 0.002 | 0.006 | |
tool.subgraph | 0.147 | 0.004 | 0.181 | |
tool.subgraph.find | 0.163 | 0.006 | 0.222 | |
tool.subgraph.search | 0.148 | 0.005 | 0.171 | |
tool.subgraph.stats | 0.183 | 0.006 | 0.221 | |
tool.translate | 0.079 | 0.010 | 0.099 | |
tool.unify | 0.003 | 0.001 | 0.004 | |