Zeyneb Kurt
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/Mergeomics |
| Branch: RELEASE_3_11 |
| Last Commit: 0046ef8 |
| Last Changed Date: 2020-04-27 14:54:28 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:02 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE Mergeomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1024/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Mergeomics 1.16.0 Zeyneb Kurt
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: Mergeomics |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mergeomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Mergeomics_1.16.0.tar.gz |
| StartedAt: 2020-10-17 05:46:54 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:05:06 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1092.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Mergeomics.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mergeomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Mergeomics_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Mergeomics.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Mergeomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mergeomics' version '1.16.0'
* 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 whether package 'Mergeomics' can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.8Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ssea.finish.fdr 9.78 0.01 9.86
kda.analyze.exec 7.79 0.10 8.20
kda.analyze.simulate 7.75 0.04 7.80
kda.analyze.test 7.57 0.00 7.56
kda.prepare 7.21 0.02 7.23
ssea2kda.analyze 6.11 0.03 6.14
ssea2kda 6.03 0.02 6.09
ssea.finish.genes 5.69 0.06 5.80
ssea.meta 5.30 0.04 5.33
ssea.analyze 4.32 0.00 5.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kda.analyze.exec 7.63 0.09 7.75
kda.prepare 7.63 0.02 7.64
kda.analyze.test 7.39 0.01 7.41
kda.analyze.simulate 6.84 0.02 6.89
ssea.meta 6.13 0.11 6.36
ssea2kda 6.20 0.02 6.22
ssea2kda.analyze 5.89 0.04 5.92
ssea.finish.fdr 5.02 0.05 5.06
ssea.analyze.simulate 5.05 0.00 5.04
ssea.finish.genes 5.00 0.01 5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.11-bioc/meat/Mergeomics.Rcheck/00check.log'
for details.
Mergeomics.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Mergeomics_1.16.0.tar.gz && rm -rf Mergeomics.buildbin-libdir && mkdir Mergeomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Mergeomics.buildbin-libdir Mergeomics_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Mergeomics_1.16.0.zip && rm Mergeomics_1.16.0.tar.gz Mergeomics_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
30 2971k 30 912k 0 0 2946k 0 0:00:01 --:--:-- 0:00:01 3000k
100 2971k 100 2971k 0 0 8857k 0 --:--:-- --:--:-- --:--:-- 9004k
install for i386
* installing *source* package 'Mergeomics' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Mergeomics'
finding HTML links ... done
MSEA.KDA.onestep html
Mergeomics-package html
job.kda html
kda.analyze html
kda.analyze.exec html
kda.analyze.simulate html
kda.analyze.test html
kda.configure html
kda.finish html
kda.finish.estimate html
kda.finish.save html
kda.finish.summarize html
kda.finish.trim html
kda.prepare html
kda.prepare.overlap html
kda.prepare.screen html
kda.start html
kda.start.edges html
kda.start.identify html
kda.start.modules html
kda2cytoscape html
kda2cytoscape.colorize html
kda2cytoscape.colormap html
kda2cytoscape.drivers html
kda2cytoscape.edges html
kda2cytoscape.exec html
kda2cytoscape.identify html
kda2himmeli html
kda2himmeli.colorize html
kda2himmeli.colormap html
kda2himmeli.drivers html
kda2himmeli.edges html
kda2himmeli.exec html
kda2himmeli.identify html
ssea.analyze html
ssea.analyze.observe html
ssea.analyze.randgenes html
ssea.analyze.randloci html
ssea.analyze.simulate html
ssea.analyze.statistic html
ssea.control html
ssea.finish html
ssea.finish.details html
ssea.finish.fdr html
ssea.finish.genes html
ssea.meta html
ssea.prepare html
ssea.prepare.counts html
ssea.prepare.structure html
ssea.start html
ssea.start.configure html
ssea.start.identify html
ssea.start.relabel html
ssea2kda html
ssea2kda.analyze html
ssea2kda.import html
tool.aggregate html
tool.cluster html
tool.cluster.static html
tool.coalesce html
tool.coalesce.exec html
tool.coalesce.find html
tool.coalesce.merge html
tool.fdr html
tool.fdr.bh html
tool.fdr.empirical html
tool.graph html
tool.graph.degree html
tool.graph.list html
tool.metap html
tool.normalize html
tool.normalize.quality html
tool.overlap html
tool.read html
tool.save html
tool.subgraph html
tool.subgraph.find html
tool.subgraph.search html
tool.subgraph.stats html
tool.translate html
tool.unify html
** 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
install for x64
* installing *source* package 'Mergeomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mergeomics' as Mergeomics_1.16.0.zip
* DONE (Mergeomics)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Mergeomics' successfully unpacked and MD5 sums checked
|
Mergeomics.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 6.586784 Mb
Minimum degree set to 20
Maximum degree set to 278
Collecting hubs...
4876 hubs (25.21%)
Graph: 10.54147 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.
112388/1673535
238970/1673535
395518/1673535
575859/1673535
743749/1673535
915773/1673535
1102706/1673535
1238542/1673535
1390262/1673535
1540392/1673535
1673535 comparisons
21115 comparisons
13861 comparisons
12880 comparisons
Job: 8.950638 Mb
Preparing data structures...
Job: 13.98173 Mb
Adding positive controls...
Job: 14.23988 Mb
Estimating enrichment...
100/100 cycles
Normalizing scores...
RUNIT TEST PROTOCOL -- Sat Oct 17 05:58:01 2020
***********************************************
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
380.64 1.00 382.03
|
Mergeomics.Rcheck/tests_x64/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
151538/1673535
302319/1673535
442401/1673535
600135/1673535
741934/1673535
905568/1673535
1018057/1673535
1161966/1673535
1310333/1673535
1462692/1673535
1617943/1673535
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 -- Sat Oct 17 06:04:53 2020
***********************************************
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
410.70 0.71 411.51
|
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Mergeomics.Rcheck/examples_i386/Mergeomics-Ex.timings
|
Mergeomics.Rcheck/examples_x64/Mergeomics-Ex.timings
|