Zeyneb Kurt
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Mergeomics |
| Branch: master |
| Last Commit: a824958 |
| Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:32:44 -0400 (Tue, 09 Apr 2019).
| Package 934/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Mergeomics 1.11.0 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: Mergeomics |
| Version: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2019-04-09 02:02:49 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:16:15 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 805.9 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_1.11.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Mergeomics.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.11.0’
* 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
ssea.meta 18.597 0.309 19.053
kda.analyze.exec 12.937 0.224 13.269
kda.analyze.test 13.005 0.149 13.282
kda.prepare 12.918 0.145 13.186
kda.analyze.simulate 12.613 0.166 12.904
ssea2kda 7.823 0.507 8.383
ssea2kda.analyze 7.617 0.476 8.169
ssea2kda.import 6.431 0.237 6.739
ssea.finish.genes 6.322 0.237 6.630
ssea.finish.details 6.337 0.219 6.639
ssea.finish 6.078 0.195 6.318
ssea.analyze 6.008 0.247 6.299
ssea.finish.fdr 5.572 0.223 5.849
ssea.analyze.simulate 5.212 0.194 5.462
ssea.prepare.counts 4.905 0.057 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
‘/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’ ... ** 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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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=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.
105489/1673535
195466/1673535
280759/1673535
372349/1673535
478492/1673535
563676/1673535
646241/1673535
727679/1673535
808918/1673535
889732/1673535
971489/1673535
1053141/1673535
1134013/1673535
1214034/1673535
1295368/1673535
1377728/1673535
1460263/1673535
1539251/1673535
1620963/1673535
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 9 02:16:04 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
562.979 9.354 580.414
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.003 | 0.001 | 0.004 | |
| job.kda | 0.022 | 0.003 | 0.025 | |
| kda.analyze | 0.015 | 0.002 | 0.023 | |
| kda.analyze.exec | 12.937 | 0.224 | 13.269 | |
| kda.analyze.simulate | 12.613 | 0.166 | 12.904 | |
| kda.analyze.test | 13.005 | 0.149 | 13.282 | |
| kda.configure | 0.002 | 0.001 | 0.002 | |
| kda.finish | 0.178 | 0.010 | 0.190 | |
| kda.finish.estimate | 0.120 | 0.006 | 0.126 | |
| kda.finish.save | 0.122 | 0.006 | 0.130 | |
| kda.finish.summarize | 0.126 | 0.007 | 0.133 | |
| kda.finish.trim | 0.103 | 0.006 | 0.113 | |
| kda.prepare | 12.918 | 0.145 | 13.186 | |
| kda.prepare.overlap | 0.000 | 0.000 | 0.001 | |
| kda.prepare.screen | 0.000 | 0.001 | 0.001 | |
| kda.start | 1.571 | 0.103 | 1.690 | |
| kda.start.edges | 0.001 | 0.001 | 0.002 | |
| kda.start.identify | 0.005 | 0.000 | 0.005 | |
| kda.start.modules | 0.001 | 0.001 | 0.002 | |
| kda2cytoscape | 0.478 | 0.011 | 0.495 | |
| kda2cytoscape.colorize | 0.000 | 0.000 | 0.001 | |
| kda2cytoscape.colormap | 0.001 | 0.000 | 0.001 | |
| kda2cytoscape.drivers | 0.184 | 0.009 | 0.194 | |
| kda2cytoscape.edges | 0.204 | 0.008 | 0.229 | |
| kda2cytoscape.exec | 0.198 | 0.010 | 0.214 | |
| kda2cytoscape.identify | 0.006 | 0.000 | 0.006 | |
| kda2himmeli | 0.454 | 0.012 | 0.467 | |
| kda2himmeli.colorize | 0 | 0 | 0 | |
| kda2himmeli.colormap | 0.000 | 0.001 | 0.001 | |
| kda2himmeli.drivers | 0.187 | 0.007 | 0.196 | |
| kda2himmeli.edges | 0.208 | 0.010 | 0.218 | |
| kda2himmeli.exec | 0.245 | 0.008 | 0.254 | |
| kda2himmeli.identify | 0.006 | 0.001 | 0.007 | |
| ssea.analyze | 6.008 | 0.247 | 6.299 | |
| ssea.analyze.observe | 4.502 | 0.049 | 4.576 | |
| ssea.analyze.randgenes | 4.243 | 0.056 | 4.327 | |
| ssea.analyze.randloci | 4.628 | 0.051 | 4.713 | |
| ssea.analyze.simulate | 5.212 | 0.194 | 5.462 | |
| ssea.analyze.statistic | 0.001 | 0.001 | 0.001 | |
| ssea.control | 4.193 | 0.050 | 4.284 | |
| ssea.finish | 6.078 | 0.195 | 6.318 | |
| ssea.finish.details | 6.337 | 0.219 | 6.639 | |
| ssea.finish.fdr | 5.572 | 0.223 | 5.849 | |
| ssea.finish.genes | 6.322 | 0.237 | 6.630 | |
| ssea.meta | 18.597 | 0.309 | 19.053 | |
| ssea.prepare | 4.857 | 0.062 | 4.973 | |
| ssea.prepare.counts | 4.905 | 0.057 | 5.015 | |
| ssea.prepare.structure | 4.604 | 0.046 | 4.681 | |
| ssea.start | 4.037 | 0.040 | 4.103 | |
| ssea.start.configure | 0.391 | 0.026 | 0.422 | |
| ssea.start.identify | 0.004 | 0.000 | 0.004 | |
| ssea.start.relabel | 3.686 | 0.038 | 3.749 | |
| ssea2kda | 7.823 | 0.507 | 8.383 | |
| ssea2kda.analyze | 7.617 | 0.476 | 8.169 | |
| ssea2kda.import | 6.431 | 0.237 | 6.739 | |
| tool.aggregate | 0.002 | 0.001 | 0.001 | |
| tool.cluster | 0.022 | 0.000 | 0.022 | |
| tool.cluster.static | 0.001 | 0.000 | 0.002 | |
| tool.coalesce | 0.065 | 0.001 | 0.066 | |
| tool.coalesce.exec | 0.161 | 0.000 | 0.161 | |
| tool.coalesce.find | 0.138 | 0.000 | 0.140 | |
| tool.coalesce.merge | 0.175 | 0.001 | 0.178 | |
| tool.fdr | 0.001 | 0.000 | 0.002 | |
| tool.fdr.bh | 0.001 | 0.000 | 0.001 | |
| tool.fdr.empirical | 0.001 | 0.000 | 0.002 | |
| tool.graph | 1.546 | 0.092 | 1.645 | |
| tool.graph.degree | 1.689 | 0.094 | 1.803 | |
| tool.graph.list | 1.675 | 0.069 | 1.764 | |
| tool.metap | 0.003 | 0.000 | 0.004 | |
| tool.normalize | 0.02 | 0.00 | 0.02 | |
| tool.normalize.quality | 0.034 | 0.002 | 0.036 | |
| tool.overlap | 0.010 | 0.000 | 0.011 | |
| tool.read | 0.258 | 0.015 | 0.274 | |
| tool.save | 0.002 | 0.001 | 0.003 | |
| tool.subgraph | 0.136 | 0.007 | 0.145 | |
| tool.subgraph.find | 0.105 | 0.009 | 0.115 | |
| tool.subgraph.search | 0.113 | 0.008 | 0.122 | |
| tool.subgraph.stats | 0.165 | 0.013 | 0.177 | |
| tool.translate | 0.056 | 0.002 | 0.059 | |
| tool.unify | 0.003 | 0.001 | 0.003 | |