Zeyneb Kurt
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Mergeomics |
| Branch: RELEASE_3_9 |
| Last Commit: 8723c7e |
| Last Changed Date: 2019-05-02 11:54:00 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:57:12 -0400 (Wed, 16 Oct 2019).
| Package 950/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Mergeomics 1.12.0 Zeyneb Kurt
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Mergeomics |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mergeomics_1.12.0.tar.gz |
| StartedAt: 2019-10-16 04:23:22 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:38:45 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 922.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Mergeomics.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mergeomics_1.12.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Mergeomics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
kda.analyze.test 13.608 0.527 14.136
kda.analyze.exec 13.442 0.657 14.101
kda.analyze.simulate 13.296 0.562 13.861
kda.prepare 12.725 0.478 13.202
ssea2kda.analyze 10.950 0.999 12.016
ssea2kda 10.291 1.252 11.550
ssea2kda.import 9.247 0.690 9.996
ssea.analyze 8.061 0.708 8.775
ssea.finish.fdr 8.036 0.661 8.698
ssea.analyze.simulate 7.904 0.648 8.553
ssea.finish.details 7.571 0.729 8.301
ssea.finish.genes 7.418 0.614 8.073
ssea.meta 7.556 0.400 7.956
ssea.finish 6.984 0.665 7.650
ssea.prepare.structure 5.818 0.087 5.905
ssea.analyze.randloci 5.659 0.080 5.739
ssea.control 5.430 0.104 5.534
ssea.analyze.randgenes 5.341 0.081 5.429
ssea.prepare 5.189 0.089 5.279
ssea.start.relabel 5.167 0.079 5.261
ssea.start 5.083 0.083 5.166
ssea.prepare.counts 5.054 0.079 5.133
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.
Mergeomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Mergeomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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=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.
72691/1673535
151976/1673535
229280/1673535
303333/1673535
397500/1673535
485436/1673535
566190/1673535
642199/1673535
723126/1673535
803705/1673535
887385/1673535
967356/1673535
1043729/1673535
1107961/1673535
1174392/1673535
1246549/1673535
1312983/1673535
1382235/1673535
1465702/1673535
1542961/1673535
1613932/1673535
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 -- Wed Oct 16 04:38:34 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
631.981 23.710 658.751
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.003 | 0.001 | 0.005 | |
| job.kda | 0.021 | 0.005 | 0.026 | |
| kda.analyze | 0.019 | 0.004 | 0.023 | |
| kda.analyze.exec | 13.442 | 0.657 | 14.101 | |
| kda.analyze.simulate | 13.296 | 0.562 | 13.861 | |
| kda.analyze.test | 13.608 | 0.527 | 14.136 | |
| kda.configure | 0.002 | 0.001 | 0.002 | |
| kda.finish | 0.228 | 0.027 | 0.256 | |
| kda.finish.estimate | 0.122 | 0.007 | 0.129 | |
| kda.finish.save | 0.116 | 0.006 | 0.123 | |
| kda.finish.summarize | 0.098 | 0.007 | 0.104 | |
| kda.finish.trim | 0.136 | 0.008 | 0.143 | |
| kda.prepare | 12.725 | 0.478 | 13.202 | |
| kda.prepare.overlap | 0.001 | 0.001 | 0.002 | |
| kda.prepare.screen | 0.001 | 0.001 | 0.002 | |
| kda.start | 1.822 | 0.192 | 2.013 | |
| kda.start.edges | 0.003 | 0.001 | 0.004 | |
| kda.start.identify | 0.012 | 0.001 | 0.013 | |
| kda.start.modules | 0.002 | 0.000 | 0.003 | |
| kda2cytoscape | 0.482 | 0.021 | 0.503 | |
| kda2cytoscape.colorize | 0.000 | 0.000 | 0.001 | |
| kda2cytoscape.colormap | 0.001 | 0.000 | 0.001 | |
| kda2cytoscape.drivers | 0.129 | 0.010 | 0.138 | |
| kda2cytoscape.edges | 0.126 | 0.011 | 0.138 | |
| kda2cytoscape.exec | 0.156 | 0.012 | 0.168 | |
| kda2cytoscape.identify | 0.007 | 0.001 | 0.008 | |
| kda2himmeli | 0.579 | 0.022 | 0.603 | |
| kda2himmeli.colorize | 0.000 | 0.000 | 0.001 | |
| kda2himmeli.colormap | 0.001 | 0.000 | 0.001 | |
| kda2himmeli.drivers | 0.210 | 0.015 | 0.225 | |
| kda2himmeli.edges | 0.181 | 0.012 | 0.192 | |
| kda2himmeli.exec | 0.340 | 0.020 | 0.361 | |
| kda2himmeli.identify | 0.008 | 0.001 | 0.010 | |
| ssea.analyze | 8.061 | 0.708 | 8.775 | |
| ssea.analyze.observe | 4.825 | 0.105 | 4.928 | |
| ssea.analyze.randgenes | 5.341 | 0.081 | 5.429 | |
| ssea.analyze.randloci | 5.659 | 0.080 | 5.739 | |
| ssea.analyze.simulate | 7.904 | 0.648 | 8.553 | |
| ssea.analyze.statistic | 0.001 | 0.001 | 0.001 | |
| ssea.control | 5.430 | 0.104 | 5.534 | |
| ssea.finish | 6.984 | 0.665 | 7.650 | |
| ssea.finish.details | 7.571 | 0.729 | 8.301 | |
| ssea.finish.fdr | 8.036 | 0.661 | 8.698 | |
| ssea.finish.genes | 7.418 | 0.614 | 8.073 | |
| ssea.meta | 7.556 | 0.400 | 7.956 | |
| ssea.prepare | 5.189 | 0.089 | 5.279 | |
| ssea.prepare.counts | 5.054 | 0.079 | 5.133 | |
| ssea.prepare.structure | 5.818 | 0.087 | 5.905 | |
| ssea.start | 5.083 | 0.083 | 5.166 | |
| ssea.start.configure | 0.381 | 0.041 | 0.422 | |
| ssea.start.identify | 0.008 | 0.000 | 0.008 | |
| ssea.start.relabel | 5.167 | 0.079 | 5.261 | |
| ssea2kda | 10.291 | 1.252 | 11.550 | |
| ssea2kda.analyze | 10.950 | 0.999 | 12.016 | |
| ssea2kda.import | 9.247 | 0.690 | 9.996 | |
| tool.aggregate | 0.002 | 0.001 | 0.004 | |
| tool.cluster | 0.032 | 0.001 | 0.032 | |
| tool.cluster.static | 0.001 | 0.001 | 0.002 | |
| tool.coalesce | 0.092 | 0.001 | 0.093 | |
| tool.coalesce.exec | 0.217 | 0.001 | 0.218 | |
| tool.coalesce.find | 0.235 | 0.001 | 0.235 | |
| tool.coalesce.merge | 0.217 | 0.001 | 0.218 | |
| tool.fdr | 0.001 | 0.001 | 0.001 | |
| tool.fdr.bh | 0.002 | 0.001 | 0.002 | |
| tool.fdr.empirical | 0.001 | 0.000 | 0.001 | |
| tool.graph | 2.112 | 0.189 | 2.301 | |
| tool.graph.degree | 2.253 | 0.177 | 2.432 | |
| tool.graph.list | 1.901 | 0.217 | 2.123 | |
| tool.metap | 0.007 | 0.001 | 0.007 | |
| tool.normalize | 0.024 | 0.001 | 0.024 | |
| tool.normalize.quality | 0.019 | 0.001 | 0.020 | |
| tool.overlap | 0.014 | 0.001 | 0.015 | |
| tool.read | 0.369 | 0.042 | 0.412 | |
| tool.save | 0.003 | 0.001 | 0.003 | |
| tool.subgraph | 0.129 | 0.011 | 0.140 | |
| tool.subgraph.find | 0.129 | 0.009 | 0.138 | |
| tool.subgraph.search | 0.129 | 0.008 | 0.137 | |
| tool.subgraph.stats | 0.152 | 0.008 | 0.160 | |
| tool.translate | 0.057 | 0.006 | 0.064 | |
| tool.unify | 0.002 | 0.001 | 0.003 | |