Zeyneb Kurt
| Snapshot Date: 2023-03-23 14:00:15 -0400 (Thu, 23 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/Mergeomics |
| git_branch: devel |
| git_last_commit: 8d2d165 |
| git_last_commit_date: 2022-11-01 11:12:53 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-24 11:06:55 -0400 (Fri, 24 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4546 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4307 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4299 |
| 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 | ||||
|
To the developers/maintainers of the Mergeomics package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1142/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Mergeomics 1.27.0 (landing page) Zeyneb Kurt
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Mergeomics |
| Version: 1.27.0 |
| 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_1.27.0.tar.gz |
| StartedAt: 2023-03-24 03:14:51 -0400 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 03:36:30 -0400 (Fri, 24 Mar 2023) |
| EllapsedTime: 1299.6 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Mergeomics.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.27.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
kda.analyze.exec 16.680 0.219 24.397
kda.analyze.test 16.385 0.136 23.552
kda.analyze.simulate 16.370 0.139 23.587
kda.prepare 16.272 0.136 23.746
ssea2kda 11.548 0.160 16.301
ssea2kda.analyze 11.366 0.151 15.787
ssea.meta 9.834 0.111 13.826
ssea.finish.details 9.302 0.096 13.188
ssea2kda.import 9.240 0.088 12.307
ssea.finish.genes 9.210 0.103 12.818
ssea.analyze 8.884 0.206 12.784
ssea.finish 8.911 0.098 12.813
ssea.finish.fdr 8.865 0.100 12.217
ssea.analyze.simulate 8.579 0.109 12.951
ssea.prepare 7.193 0.045 9.949
ssea.analyze.randgenes 7.107 0.044 10.295
ssea.control 6.955 0.046 10.461
ssea.analyze.observe 6.914 0.039 10.000
ssea.analyze.randloci 6.747 0.038 9.878
ssea.prepare.counts 6.717 0.040 9.352
ssea.prepare.structure 6.671 0.042 9.335
ssea.start.relabel 6.580 0.054 8.863
ssea.start 6.400 0.044 8.893
* 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-3.17-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/4.3/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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...
3740 hubs (15057 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.
51099/1673535
102797/1673535
154735/1673535
205977/1673535
257888/1673535
309474/1673535
360691/1673535
411584/1673535
462988/1673535
515039/1673535
566995/1673535
618985/1673535
671328/1673535
724209/1673535
777140/1673535
829268/1673535
880950/1673535
932533/1673535
984093/1673535
1034432/1673535
1084003/1673535
1134695/1673535
1185901/1673535
1238192/1673535
1290350/1673535
1341787/1673535
1394112/1673535
1446227/1673535
1496244/1673535
1546071/1673535
1594935/1673535
1644966/1673535
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 -- Fri Mar 24 03:36:11 2023
***********************************************
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
651.128 10.042 883.760
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.003 | 0.001 | 0.004 | |
| job.kda | 0.027 | 0.005 | 0.051 | |
| kda.analyze | 0.017 | 0.003 | 0.028 | |
| kda.analyze.exec | 16.680 | 0.219 | 24.397 | |
| kda.analyze.simulate | 16.370 | 0.139 | 23.587 | |
| kda.analyze.test | 16.385 | 0.136 | 23.552 | |
| kda.configure | 0.001 | 0.000 | 0.001 | |
| kda.finish | 0.231 | 0.010 | 0.335 | |
| kda.finish.estimate | 0.145 | 0.003 | 0.213 | |
| kda.finish.save | 0.145 | 0.003 | 0.222 | |
| kda.finish.summarize | 0.143 | 0.003 | 0.347 | |
| kda.finish.trim | 0.151 | 0.003 | 0.169 | |
| kda.prepare | 16.272 | 0.136 | 23.746 | |
| kda.prepare.overlap | 0.001 | 0.000 | 0.001 | |
| kda.prepare.screen | 0.000 | 0.000 | 0.001 | |
| kda.start | 2.396 | 0.035 | 3.300 | |
| kda.start.edges | 0.002 | 0.001 | 0.008 | |
| kda.start.identify | 0.008 | 0.001 | 0.009 | |
| kda.start.modules | 0.003 | 0.001 | 0.003 | |
| kda2cytoscape | 0.669 | 0.011 | 0.964 | |
| kda2cytoscape.colorize | 0.001 | 0.000 | 0.001 | |
| kda2cytoscape.colormap | 0.001 | 0.000 | 0.001 | |
| kda2cytoscape.drivers | 0.241 | 0.008 | 0.369 | |
| kda2cytoscape.edges | 0.226 | 0.008 | 0.342 | |
| kda2cytoscape.exec | 0.279 | 0.009 | 0.438 | |
| kda2cytoscape.identify | 0.006 | 0.000 | 0.011 | |
| kda2himmeli | 0.685 | 0.011 | 1.001 | |
| kda2himmeli.colorize | 0 | 0 | 0 | |
| kda2himmeli.colormap | 0.000 | 0.000 | 0.001 | |
| kda2himmeli.drivers | 0.237 | 0.007 | 0.352 | |
| kda2himmeli.edges | 0.238 | 0.006 | 0.348 | |
| kda2himmeli.exec | 0.392 | 0.009 | 0.579 | |
| kda2himmeli.identify | 0.007 | 0.001 | 0.017 | |
| ssea.analyze | 8.884 | 0.206 | 12.784 | |
| ssea.analyze.observe | 6.914 | 0.039 | 10.000 | |
| ssea.analyze.randgenes | 7.107 | 0.044 | 10.295 | |
| ssea.analyze.randloci | 6.747 | 0.038 | 9.878 | |
| ssea.analyze.simulate | 8.579 | 0.109 | 12.951 | |
| ssea.analyze.statistic | 0.000 | 0.001 | 0.000 | |
| ssea.control | 6.955 | 0.046 | 10.461 | |
| ssea.finish | 8.911 | 0.098 | 12.813 | |
| ssea.finish.details | 9.302 | 0.096 | 13.188 | |
| ssea.finish.fdr | 8.865 | 0.100 | 12.217 | |
| ssea.finish.genes | 9.210 | 0.103 | 12.818 | |
| ssea.meta | 9.834 | 0.111 | 13.826 | |
| ssea.prepare | 7.193 | 0.045 | 9.949 | |
| ssea.prepare.counts | 6.717 | 0.040 | 9.352 | |
| ssea.prepare.structure | 6.671 | 0.042 | 9.335 | |
| ssea.start | 6.400 | 0.044 | 8.893 | |
| ssea.start.configure | 0.612 | 0.015 | 0.823 | |
| ssea.start.identify | 0.007 | 0.001 | 0.009 | |
| ssea.start.relabel | 6.580 | 0.054 | 8.863 | |
| ssea2kda | 11.548 | 0.160 | 16.301 | |
| ssea2kda.analyze | 11.366 | 0.151 | 15.787 | |
| ssea2kda.import | 9.240 | 0.088 | 12.307 | |
| tool.aggregate | 0.001 | 0.001 | 0.002 | |
| tool.cluster | 0.031 | 0.001 | 0.038 | |
| tool.cluster.static | 0.001 | 0.000 | 0.001 | |
| tool.coalesce | 0.092 | 0.001 | 0.122 | |
| tool.coalesce.exec | 0.240 | 0.001 | 0.311 | |
| tool.coalesce.find | 0.233 | 0.001 | 0.304 | |
| tool.coalesce.merge | 0.246 | 0.002 | 0.324 | |
| tool.fdr | 0.001 | 0.000 | 0.001 | |
| tool.fdr.bh | 0.001 | 0.000 | 0.001 | |
| tool.fdr.empirical | 0.001 | 0.000 | 0.001 | |
| tool.graph | 2.351 | 0.034 | 3.149 | |
| tool.graph.degree | 2.503 | 0.034 | 3.349 | |
| tool.graph.list | 2.388 | 0.033 | 3.187 | |
| tool.metap | 0.005 | 0.000 | 0.009 | |
| tool.normalize | 0.034 | 0.004 | 0.050 | |
| tool.normalize.quality | 0.019 | 0.000 | 0.027 | |
| tool.overlap | 0.012 | 0.001 | 0.016 | |
| tool.read | 0.384 | 0.007 | 0.523 | |
| tool.save | 0.001 | 0.000 | 0.003 | |
| tool.subgraph | 0.149 | 0.002 | 0.207 | |
| tool.subgraph.find | 0.146 | 0.003 | 0.209 | |
| tool.subgraph.search | 0.150 | 0.003 | 0.205 | |
| tool.subgraph.stats | 0.171 | 0.003 | 0.230 | |
| tool.translate | 0.071 | 0.007 | 0.103 | |
| tool.unify | 0.002 | 0.000 | 0.002 | |