Zeyneb Kurt
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/Mergeomics |
| git_branch: RELEASE_3_22 |
| git_last_commit: a71f54d |
| git_last_commit_date: 2025-10-29 10:29:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-08 12:01 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1231/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Mergeomics 1.38.0 (landing page) Zeyneb Kurt
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.38.0 |
| 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_1.38.0.tar.gz |
| StartedAt: 2025-12-05 07:14:32 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 07:39:37 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 1505.2 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Mergeomics.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.38.0’
* 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 ... INFO
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.exec 19.338 0.407 24.681
kda.prepare 19.067 0.315 23.936
kda.analyze.test 19.047 0.308 23.783
kda.analyze.simulate 18.833 0.308 23.554
ssea2kda.analyze 13.960 0.251 17.314
ssea2kda 13.727 0.231 17.722
ssea2kda.import 12.122 0.168 15.254
ssea.analyze 11.955 0.255 15.363
ssea.finish.fdr 11.902 0.162 15.489
ssea.finish.details 11.776 0.154 15.518
ssea.finish 11.744 0.160 15.006
ssea.meta 11.588 0.180 15.188
ssea.finish.genes 11.514 0.176 15.178
ssea.analyze.simulate 11.252 0.176 15.469
ssea.analyze.randgenes 9.831 0.085 13.350
ssea.analyze.observe 9.494 0.098 12.079
ssea.prepare 9.367 0.084 12.123
ssea.start.relabel 9.193 0.086 12.291
ssea.control 9.186 0.075 11.886
ssea.analyze.randloci 9.174 0.084 12.454
ssea.prepare.counts 9.166 0.073 11.332
ssea.prepare.structure 9.042 0.079 11.578
ssea.start 9.017 0.069 11.202
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘Mergeomics’ ... ** this is package ‘Mergeomics’ version ‘1.38.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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...
3858 hubs (15434 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.
33932/1673535
68057/1673535
102893/1673535
137325/1673535
171100/1673535
202014/1673535
233054/1673535
265160/1673535
296885/1673535
329085/1673535
360856/1673535
395747/1673535
433647/1673535
473442/1673535
507852/1673535
543318/1673535
578708/1673535
612715/1673535
649480/1673535
686006/1673535
722463/1673535
758626/1673535
794283/1673535
830215/1673535
866165/1673535
902066/1673535
938903/1673535
974545/1673535
1010196/1673535
1045895/1673535
1082457/1673535
1119193/1673535
1155466/1673535
1192523/1673535
1228569/1673535
1264240/1673535
1299866/1673535
1336308/1673535
1372219/1673535
1407588/1673535
1442680/1673535
1478767/1673535
1512681/1673535
1548803/1673535
1585217/1673535
1620179/1673535
1656000/1673535
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 -- Fri Dec 5 07:39:07 2025
***********************************************
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
807.916 15.703 1035.434
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.005 | 0.004 | 0.010 | |
| job.kda | 0.029 | 0.007 | 0.040 | |
| kda.analyze | 0.018 | 0.006 | 0.026 | |
| kda.analyze.exec | 19.338 | 0.407 | 24.681 | |
| kda.analyze.simulate | 18.833 | 0.308 | 23.554 | |
| kda.analyze.test | 19.047 | 0.308 | 23.783 | |
| kda.configure | 0.001 | 0.001 | 0.003 | |
| kda.finish | 0.247 | 0.024 | 0.326 | |
| kda.finish.estimate | 0.129 | 0.006 | 0.162 | |
| kda.finish.save | 0.132 | 0.007 | 0.174 | |
| kda.finish.summarize | 0.131 | 0.008 | 0.165 | |
| kda.finish.trim | 0.130 | 0.007 | 0.172 | |
| kda.prepare | 19.067 | 0.315 | 23.936 | |
| kda.prepare.overlap | 0.001 | 0.003 | 0.003 | |
| kda.prepare.screen | 0.001 | 0.002 | 0.004 | |
| kda.start | 2.528 | 0.062 | 3.052 | |
| kda.start.edges | 0.003 | 0.002 | 0.006 | |
| kda.start.identify | 0.009 | 0.002 | 0.011 | |
| kda.start.modules | 0.004 | 0.003 | 0.006 | |
| kda2cytoscape | 0.723 | 0.020 | 0.875 | |
| kda2cytoscape.colorize | 0.000 | 0.001 | 0.001 | |
| kda2cytoscape.colormap | 0.001 | 0.001 | 0.001 | |
| kda2cytoscape.drivers | 0.241 | 0.015 | 0.314 | |
| kda2cytoscape.edges | 0.248 | 0.017 | 0.322 | |
| kda2cytoscape.exec | 0.286 | 0.016 | 0.390 | |
| kda2cytoscape.identify | 0.007 | 0.001 | 0.016 | |
| kda2himmeli | 0.743 | 0.026 | 0.935 | |
| kda2himmeli.colorize | 0.000 | 0.000 | 0.001 | |
| kda2himmeli.colormap | 0.001 | 0.001 | 0.001 | |
| kda2himmeli.drivers | 0.236 | 0.015 | 0.312 | |
| kda2himmeli.edges | 0.244 | 0.016 | 0.316 | |
| kda2himmeli.exec | 0.383 | 0.018 | 0.493 | |
| kda2himmeli.identify | 0.007 | 0.001 | 0.011 | |
| ssea.analyze | 11.955 | 0.255 | 15.363 | |
| ssea.analyze.observe | 9.494 | 0.098 | 12.079 | |
| ssea.analyze.randgenes | 9.831 | 0.085 | 13.350 | |
| ssea.analyze.randloci | 9.174 | 0.084 | 12.454 | |
| ssea.analyze.simulate | 11.252 | 0.176 | 15.469 | |
| ssea.analyze.statistic | 0.000 | 0.001 | 0.001 | |
| ssea.control | 9.186 | 0.075 | 11.886 | |
| ssea.finish | 11.744 | 0.160 | 15.006 | |
| ssea.finish.details | 11.776 | 0.154 | 15.518 | |
| ssea.finish.fdr | 11.902 | 0.162 | 15.489 | |
| ssea.finish.genes | 11.514 | 0.176 | 15.178 | |
| ssea.meta | 11.588 | 0.180 | 15.188 | |
| ssea.prepare | 9.367 | 0.084 | 12.123 | |
| ssea.prepare.counts | 9.166 | 0.073 | 11.332 | |
| ssea.prepare.structure | 9.042 | 0.079 | 11.578 | |
| ssea.start | 9.017 | 0.069 | 11.202 | |
| ssea.start.configure | 0.606 | 0.027 | 0.794 | |
| ssea.start.identify | 0.007 | 0.003 | 0.014 | |
| ssea.start.relabel | 9.193 | 0.086 | 12.291 | |
| ssea2kda | 13.727 | 0.231 | 17.722 | |
| ssea2kda.analyze | 13.960 | 0.251 | 17.314 | |
| ssea2kda.import | 12.122 | 0.168 | 15.254 | |
| tool.aggregate | 0.003 | 0.003 | 0.005 | |
| tool.cluster | 0.037 | 0.002 | 0.048 | |
| tool.cluster.static | 0.001 | 0.001 | 0.002 | |
| tool.coalesce | 0.085 | 0.003 | 0.108 | |
| tool.coalesce.exec | 0.299 | 0.003 | 0.365 | |
| tool.coalesce.find | 0.306 | 0.003 | 0.379 | |
| tool.coalesce.merge | 0.361 | 0.010 | 0.453 | |
| tool.fdr | 0.001 | 0.001 | 0.002 | |
| tool.fdr.bh | 0.001 | 0.000 | 0.002 | |
| tool.fdr.empirical | 0.001 | 0.001 | 0.006 | |
| tool.graph | 2.318 | 0.051 | 2.899 | |
| tool.graph.degree | 2.308 | 0.059 | 2.907 | |
| tool.graph.list | 2.258 | 0.051 | 2.825 | |
| tool.metap | 0.006 | 0.002 | 0.009 | |
| tool.normalize | 0.043 | 0.002 | 0.063 | |
| tool.normalize.quality | 0.022 | 0.002 | 0.026 | |
| tool.overlap | 0.015 | 0.003 | 0.022 | |
| tool.read | 0.385 | 0.013 | 0.496 | |
| tool.save | 0.002 | 0.001 | 0.006 | |
| tool.subgraph | 0.134 | 0.006 | 0.174 | |
| tool.subgraph.find | 0.134 | 0.006 | 0.171 | |
| tool.subgraph.search | 0.135 | 0.007 | 0.175 | |
| tool.subgraph.stats | 0.164 | 0.008 | 0.213 | |
| tool.translate | 0.059 | 0.002 | 0.076 | |
| tool.unify | 0.002 | 0.001 | 0.003 | |