Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | ![]() | ||||||||
palomino3 | 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: 2024-06-24 07:07:54 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 07:28:40 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1246.4 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 4.4.0 (2024-04-24) * 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 18.811 0.376 21.598 kda.analyze.simulate 18.858 0.309 21.920 kda.analyze.test 18.787 0.273 21.646 kda.prepare 18.561 0.279 22.180 ssea2kda 12.499 0.258 14.478 ssea2kda.analyze 12.304 0.266 14.998 ssea.meta 10.469 0.193 11.830 ssea2kda.import 10.167 0.173 11.739 ssea.finish.details 10.044 0.177 11.428 ssea.analyze 9.941 0.250 11.262 ssea.finish.genes 9.869 0.188 11.113 ssea.finish 9.818 0.168 11.384 ssea.finish.fdr 9.803 0.181 11.092 ssea.analyze.simulate 9.218 0.173 10.496 ssea.prepare 7.645 0.091 8.971 ssea.analyze.randloci 7.623 0.085 8.611 ssea.analyze.randgenes 7.616 0.087 8.439 ssea.analyze.observe 7.540 0.085 8.635 ssea.control 7.407 0.084 8.259 ssea.prepare.counts 7.287 0.078 8.099 ssea.prepare.structure 7.275 0.077 8.137 ssea.start 7.249 0.081 8.220 ssea.start.relabel 7.115 0.078 7.902 * 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 4.4.0 (2024-04-24) -- "Puppy Cup" 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... 4200 hubs (16444 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. 45272/1673535 95713/1673535 148163/1673535 199363/1673535 249406/1673535 300958/1673535 350378/1673535 399742/1673535 450670/1673535 500282/1673535 555988/1673535 608416/1673535 660956/1673535 710153/1673535 760633/1673535 811535/1673535 863241/1673535 916420/1673535 969494/1673535 1023731/1673535 1083840/1673535 1139392/1673535 1195442/1673535 1252785/1673535 1308952/1673535 1364404/1673535 1417731/1673535 1473671/1673535 1528643/1673535 1580915/1673535 1639802/1673535 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 Jun 24 07:28:13 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 721.889 17.736 861.614
Mergeomics.Rcheck/Mergeomics-Ex.timings
name | user | system | elapsed | |
MSEA.KDA.onestep | 0.005 | 0.004 | 0.012 | |
job.kda | 0.029 | 0.008 | 0.043 | |
kda.analyze | 0.019 | 0.006 | 0.052 | |
kda.analyze.exec | 18.811 | 0.376 | 21.598 | |
kda.analyze.simulate | 18.858 | 0.309 | 21.920 | |
kda.analyze.test | 18.787 | 0.273 | 21.646 | |
kda.configure | 0.001 | 0.001 | 0.003 | |
kda.finish | 0.237 | 0.017 | 0.320 | |
kda.finish.estimate | 0.138 | 0.005 | 0.162 | |
kda.finish.save | 0.139 | 0.004 | 0.165 | |
kda.finish.summarize | 0.139 | 0.004 | 0.165 | |
kda.finish.trim | 0.138 | 0.005 | 0.164 | |
kda.prepare | 18.561 | 0.279 | 22.180 | |
kda.prepare.overlap | 0.001 | 0.001 | 0.003 | |
kda.prepare.screen | 0.000 | 0.001 | 0.002 | |
kda.start | 2.579 | 0.077 | 3.105 | |
kda.start.edges | 0.004 | 0.003 | 0.006 | |
kda.start.identify | 0.009 | 0.002 | 0.012 | |
kda.start.modules | 0.004 | 0.003 | 0.013 | |
kda2cytoscape | 0.725 | 0.021 | 0.841 | |
kda2cytoscape.colorize | 0.000 | 0.001 | 0.001 | |
kda2cytoscape.colormap | 0.001 | 0.000 | 0.001 | |
kda2cytoscape.drivers | 0.299 | 0.016 | 0.354 | |
kda2cytoscape.edges | 0.227 | 0.012 | 0.277 | |
kda2cytoscape.exec | 0.282 | 0.016 | 0.339 | |
kda2cytoscape.identify | 0.008 | 0.001 | 0.012 | |
kda2himmeli | 0.745 | 0.023 | 0.875 | |
kda2himmeli.colorize | 0.000 | 0.000 | 0.001 | |
kda2himmeli.colormap | 0.001 | 0.000 | 0.001 | |
kda2himmeli.drivers | 0.231 | 0.013 | 0.263 | |
kda2himmeli.edges | 0.237 | 0.012 | 0.268 | |
kda2himmeli.exec | 0.366 | 0.015 | 0.406 | |
kda2himmeli.identify | 0.007 | 0.001 | 0.010 | |
ssea.analyze | 9.941 | 0.250 | 11.262 | |
ssea.analyze.observe | 7.540 | 0.085 | 8.635 | |
ssea.analyze.randgenes | 7.616 | 0.087 | 8.439 | |
ssea.analyze.randloci | 7.623 | 0.085 | 8.611 | |
ssea.analyze.simulate | 9.218 | 0.173 | 10.496 | |
ssea.analyze.statistic | 0.001 | 0.001 | 0.002 | |
ssea.control | 7.407 | 0.084 | 8.259 | |
ssea.finish | 9.818 | 0.168 | 11.384 | |
ssea.finish.details | 10.044 | 0.177 | 11.428 | |
ssea.finish.fdr | 9.803 | 0.181 | 11.092 | |
ssea.finish.genes | 9.869 | 0.188 | 11.113 | |
ssea.meta | 10.469 | 0.193 | 11.830 | |
ssea.prepare | 7.645 | 0.091 | 8.971 | |
ssea.prepare.counts | 7.287 | 0.078 | 8.099 | |
ssea.prepare.structure | 7.275 | 0.077 | 8.137 | |
ssea.start | 7.249 | 0.081 | 8.220 | |
ssea.start.configure | 0.606 | 0.029 | 0.736 | |
ssea.start.identify | 0.007 | 0.002 | 0.011 | |
ssea.start.relabel | 7.115 | 0.078 | 7.902 | |
ssea2kda | 12.499 | 0.258 | 14.478 | |
ssea2kda.analyze | 12.304 | 0.266 | 14.998 | |
ssea2kda.import | 10.167 | 0.173 | 11.739 | |
tool.aggregate | 0.002 | 0.003 | 0.005 | |
tool.cluster | 0.033 | 0.002 | 0.044 | |
tool.cluster.static | 0.001 | 0.001 | 0.002 | |
tool.coalesce | 0.088 | 0.003 | 0.102 | |
tool.coalesce.exec | 0.260 | 0.002 | 0.289 | |
tool.coalesce.find | 0.254 | 0.004 | 0.294 | |
tool.coalesce.merge | 0.262 | 0.003 | 0.291 | |
tool.fdr | 0.001 | 0.001 | 0.002 | |
tool.fdr.bh | 0.002 | 0.001 | 0.003 | |
tool.fdr.empirical | 0.001 | 0.000 | 0.001 | |
tool.graph | 2.461 | 0.059 | 2.855 | |
tool.graph.degree | 2.641 | 0.069 | 3.069 | |
tool.graph.list | 2.440 | 0.063 | 2.874 | |
tool.metap | 0.006 | 0.002 | 0.009 | |
tool.normalize | 0.028 | 0.001 | 0.033 | |
tool.normalize.quality | 0.022 | 0.001 | 0.024 | |
tool.overlap | 0.014 | 0.002 | 0.017 | |
tool.read | 0.401 | 0.012 | 0.459 | |
tool.save | 0.002 | 0.002 | 0.004 | |
tool.subgraph | 0.140 | 0.004 | 0.184 | |
tool.subgraph.find | 0.140 | 0.005 | 0.157 | |
tool.subgraph.search | 0.143 | 0.004 | 0.156 | |
tool.subgraph.stats | 0.174 | 0.006 | 0.197 | |
tool.translate | 0.064 | 0.003 | 0.074 | |
tool.unify | 0.002 | 0.000 | 0.002 | |