Zeyneb Kurt
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/Mergeomics |
| git_branch: RELEASE_3_19 |
| git_last_commit: 2d045ec |
| git_last_commit_date: 2024-04-30 10:48:10 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 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" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2024-06-10 21:02:01 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 21:14:06 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 725.2 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: aarch64-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 Ventura 13.6.5
* 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.simulate 8.395 0.284 13.202
kda.analyze.exec 8.357 0.275 13.227
kda.analyze.test 8.121 0.247 12.422
kda.prepare 7.977 0.245 11.382
ssea2kda.analyze 6.688 0.271 10.282
ssea2kda 6.591 0.294 9.594
ssea.meta 5.617 0.188 8.821
ssea.finish.details 5.026 0.179 7.690
ssea.finish.fdr 4.959 0.172 7.762
ssea.analyze 4.859 0.176 7.576
ssea.finish.genes 4.830 0.176 7.680
ssea.finish 4.818 0.158 7.487
ssea2kda.import 4.768 0.180 6.614
ssea.analyze.simulate 4.716 0.157 7.542
ssea.prepare 3.645 0.073 5.750
ssea.analyze.randloci 3.510 0.077 5.375
ssea.analyze.observe 3.406 0.062 5.172
ssea.analyze.randgenes 3.356 0.060 5.193
ssea.control 3.350 0.064 5.200
* 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-arm64/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: aarch64-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...
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.
117830/1673535
239419/1673535
360559/1673535
483983/1673535
603713/1673535
726343/1673535
844832/1673535
965788/1673535
1088670/1673535
1215242/1673535
1335589/1673535
1457930/1673535
1577038/1673535
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 10 21:13:39 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
294.106 13.401 461.146
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.002 | 0.001 | 0.004 | |
| job.kda | 0.016 | 0.006 | 0.033 | |
| kda.analyze | 0.010 | 0.004 | 0.018 | |
| kda.analyze.exec | 8.357 | 0.275 | 13.227 | |
| kda.analyze.simulate | 8.395 | 0.284 | 13.202 | |
| kda.analyze.test | 8.121 | 0.247 | 12.422 | |
| kda.configure | 0.000 | 0.001 | 0.001 | |
| kda.finish | 0.107 | 0.011 | 0.177 | |
| kda.finish.estimate | 0.070 | 0.002 | 0.115 | |
| kda.finish.save | 0.070 | 0.003 | 0.127 | |
| kda.finish.summarize | 0.069 | 0.003 | 0.102 | |
| kda.finish.trim | 0.069 | 0.003 | 0.119 | |
| kda.prepare | 7.977 | 0.245 | 11.382 | |
| kda.prepare.overlap | 0.000 | 0.001 | 0.000 | |
| kda.prepare.screen | 0.001 | 0.001 | 0.001 | |
| kda.start | 1.626 | 0.064 | 2.520 | |
| kda.start.edges | 0.002 | 0.002 | 0.004 | |
| kda.start.identify | 0.004 | 0.001 | 0.009 | |
| kda.start.modules | 0.001 | 0.001 | 0.002 | |
| kda2cytoscape | 0.299 | 0.015 | 0.468 | |
| kda2cytoscape.colorize | 0 | 0 | 0 | |
| kda2cytoscape.colormap | 0 | 0 | 0 | |
| kda2cytoscape.drivers | 0.117 | 0.010 | 0.187 | |
| kda2cytoscape.edges | 0.105 | 0.010 | 0.148 | |
| kda2cytoscape.exec | 0.138 | 0.012 | 0.217 | |
| kda2cytoscape.identify | 0.004 | 0.001 | 0.010 | |
| kda2himmeli | 0.357 | 0.018 | 0.567 | |
| kda2himmeli.colorize | 0 | 0 | 0 | |
| kda2himmeli.colormap | 0.001 | 0.000 | 0.001 | |
| kda2himmeli.drivers | 0.121 | 0.012 | 0.194 | |
| kda2himmeli.edges | 0.122 | 0.011 | 0.230 | |
| kda2himmeli.exec | 0.319 | 0.021 | 0.512 | |
| kda2himmeli.identify | 0.003 | 0.000 | 0.005 | |
| ssea.analyze | 4.859 | 0.176 | 7.576 | |
| ssea.analyze.observe | 3.406 | 0.062 | 5.172 | |
| ssea.analyze.randgenes | 3.356 | 0.060 | 5.193 | |
| ssea.analyze.randloci | 3.510 | 0.077 | 5.375 | |
| ssea.analyze.simulate | 4.716 | 0.157 | 7.542 | |
| ssea.analyze.statistic | 0.000 | 0.000 | 0.001 | |
| ssea.control | 3.350 | 0.064 | 5.200 | |
| ssea.finish | 4.818 | 0.158 | 7.487 | |
| ssea.finish.details | 5.026 | 0.179 | 7.690 | |
| ssea.finish.fdr | 4.959 | 0.172 | 7.762 | |
| ssea.finish.genes | 4.830 | 0.176 | 7.680 | |
| ssea.meta | 5.617 | 0.188 | 8.821 | |
| ssea.prepare | 3.645 | 0.073 | 5.750 | |
| ssea.prepare.counts | 3.139 | 0.058 | 4.786 | |
| ssea.prepare.structure | 3.049 | 0.057 | 4.516 | |
| ssea.start | 3.128 | 0.059 | 4.778 | |
| ssea.start.configure | 0.384 | 0.020 | 0.556 | |
| ssea.start.identify | 0.004 | 0.001 | 0.004 | |
| ssea.start.relabel | 2.974 | 0.057 | 4.330 | |
| ssea2kda | 6.591 | 0.294 | 9.594 | |
| ssea2kda.analyze | 6.688 | 0.271 | 10.282 | |
| ssea2kda.import | 4.768 | 0.180 | 6.614 | |
| tool.aggregate | 0.000 | 0.001 | 0.002 | |
| tool.cluster | 0.014 | 0.001 | 0.016 | |
| tool.cluster.static | 0.000 | 0.000 | 0.001 | |
| tool.coalesce | 0.029 | 0.001 | 0.031 | |
| tool.coalesce.exec | 0.096 | 0.002 | 0.097 | |
| tool.coalesce.find | 0.103 | 0.005 | 0.108 | |
| tool.coalesce.merge | 0.100 | 0.002 | 0.163 | |
| tool.fdr | 0.000 | 0.001 | 0.000 | |
| tool.fdr.bh | 0.000 | 0.000 | 0.001 | |
| tool.fdr.empirical | 0.000 | 0.000 | 0.001 | |
| tool.graph | 1.354 | 0.053 | 1.800 | |
| tool.graph.degree | 1.586 | 0.059 | 2.315 | |
| tool.graph.list | 1.696 | 0.053 | 2.497 | |
| tool.metap | 0.003 | 0.001 | 0.003 | |
| tool.normalize | 0.042 | 0.003 | 0.069 | |
| tool.normalize.quality | 0.021 | 0.000 | 0.026 | |
| tool.overlap | 0.011 | 0.001 | 0.016 | |
| tool.read | 0.254 | 0.011 | 0.392 | |
| tool.save | 0.003 | 0.001 | 0.003 | |
| tool.subgraph | 0.086 | 0.003 | 0.117 | |
| tool.subgraph.find | 0.083 | 0.003 | 0.123 | |
| tool.subgraph.search | 0.079 | 0.003 | 0.114 | |
| tool.subgraph.stats | 0.138 | 0.005 | 0.234 | |
| tool.translate | 0.044 | 0.002 | 0.060 | |
| tool.unify | 0.001 | 0.000 | 0.002 | |