Zeyneb Kurt
| Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 Nov 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 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Mergeomics |
| Version: 1.38.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Mergeomics_1.38.0.tar.gz |
| StartedAt: 2025-11-11 11:27:26 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 11:42:48 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 922.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Mergeomics.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Mergeomics_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Mergeomics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 8.4Mb
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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ssea2kda 13.025 0.012 13.073
ssea2kda.analyze 12.819 0.008 12.862
kda.analyze.exec 12.527 0.039 12.599
kda.analyze.simulate 12.250 0.008 12.290
kda.analyze.test 11.815 0.000 11.844
kda.prepare 11.595 0.004 11.628
ssea.analyze 9.389 0.016 9.436
ssea2kda.import 9.332 0.020 9.375
ssea.finish.details 9.311 0.016 9.349
ssea.analyze.simulate 9.184 0.004 9.211
ssea.finish.genes 9.058 0.008 9.088
ssea.finish 9.028 0.008 9.057
ssea.finish.fdr 8.789 0.000 8.811
ssea.meta 8.315 0.016 8.348
ssea.analyze.randgenes 6.411 0.012 6.444
ssea.analyze.observe 5.711 0.016 5.741
ssea.analyze.randloci 5.709 0.008 5.731
ssea.control 5.652 0.012 5.678
ssea.prepare 5.323 0.004 5.340
ssea.prepare.structure 5.018 0.004 5.035
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.
Mergeomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Mergeomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
79804/1673535
160239/1673535
240047/1673535
321843/1673535
404724/1673535
489391/1673535
573036/1673535
655019/1673535
736834/1673535
819239/1673535
904304/1673535
989122/1673535
1072386/1673535
1155662/1673535
1238831/1673535
1321142/1673535
1403251/1673535
1485374/1673535
1568769/1673535
1652015/1673535
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...
46/100 cycles
93/100 cycles
100/100 cycles
Normalizing scores...
RUNIT TEST PROTOCOL -- Tue Nov 11 11:42:41 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
682.368 0.251 684.333
Mergeomics.Rcheck/Mergeomics-Ex.timings
| name | user | system | elapsed | |
| MSEA.KDA.onestep | 0.004 | 0.000 | 0.004 | |
| job.kda | 0.019 | 0.000 | 0.019 | |
| kda.analyze | 0.010 | 0.000 | 0.013 | |
| kda.analyze.exec | 12.527 | 0.039 | 12.599 | |
| kda.analyze.simulate | 12.250 | 0.008 | 12.290 | |
| kda.analyze.test | 11.815 | 0.000 | 11.844 | |
| kda.configure | 0.001 | 0.000 | 0.000 | |
| kda.finish | 0.126 | 0.008 | 0.133 | |
| kda.finish.estimate | 0.07 | 0.00 | 0.07 | |
| kda.finish.save | 0.07 | 0.00 | 0.07 | |
| kda.finish.summarize | 0.066 | 0.004 | 0.070 | |
| kda.finish.trim | 0.066 | 0.004 | 0.070 | |
| kda.prepare | 11.595 | 0.004 | 11.628 | |
| kda.prepare.overlap | 0 | 0 | 0 | |
| kda.prepare.screen | 0 | 0 | 0 | |
| kda.start | 1.532 | 0.008 | 1.544 | |
| kda.start.edges | 0.002 | 0.000 | 0.002 | |
| kda.start.identify | 0.005 | 0.000 | 0.005 | |
| kda.start.modules | 0.001 | 0.001 | 0.002 | |
| kda2cytoscape | 0.425 | 0.002 | 0.429 | |
| kda2cytoscape.colorize | 0 | 0 | 0 | |
| kda2cytoscape.colormap | 0.001 | 0.000 | 0.000 | |
| kda2cytoscape.drivers | 0.135 | 0.000 | 0.136 | |
| kda2cytoscape.edges | 0.146 | 0.000 | 0.147 | |
| kda2cytoscape.exec | 0.163 | 0.000 | 0.164 | |
| kda2cytoscape.identify | 0.005 | 0.000 | 0.006 | |
| kda2himmeli | 0.464 | 0.000 | 0.467 | |
| kda2himmeli.colorize | 0 | 0 | 0 | |
| kda2himmeli.colormap | 0 | 0 | 0 | |
| kda2himmeli.drivers | 0.131 | 0.000 | 0.131 | |
| kda2himmeli.edges | 0.140 | 0.000 | 0.139 | |
| kda2himmeli.exec | 0.238 | 0.000 | 0.239 | |
| kda2himmeli.identify | 0.005 | 0.000 | 0.005 | |
| ssea.analyze | 9.389 | 0.016 | 9.436 | |
| ssea.analyze.observe | 5.711 | 0.016 | 5.741 | |
| ssea.analyze.randgenes | 6.411 | 0.012 | 6.444 | |
| ssea.analyze.randloci | 5.709 | 0.008 | 5.731 | |
| ssea.analyze.simulate | 9.184 | 0.004 | 9.211 | |
| ssea.analyze.statistic | 0 | 0 | 0 | |
| ssea.control | 5.652 | 0.012 | 5.678 | |
| ssea.finish | 9.028 | 0.008 | 9.057 | |
| ssea.finish.details | 9.311 | 0.016 | 9.349 | |
| ssea.finish.fdr | 8.789 | 0.000 | 8.811 | |
| ssea.finish.genes | 9.058 | 0.008 | 9.088 | |
| ssea.meta | 8.315 | 0.016 | 8.348 | |
| ssea.prepare | 5.323 | 0.004 | 5.340 | |
| ssea.prepare.counts | 4.678 | 0.000 | 4.691 | |
| ssea.prepare.structure | 5.018 | 0.004 | 5.035 | |
| ssea.start | 4.805 | 0.000 | 4.818 | |
| ssea.start.configure | 0.325 | 0.008 | 0.334 | |
| ssea.start.identify | 0.004 | 0.000 | 0.004 | |
| ssea.start.relabel | 4.933 | 0.000 | 4.947 | |
| ssea2kda | 13.025 | 0.012 | 13.073 | |
| ssea2kda.analyze | 12.819 | 0.008 | 12.862 | |
| ssea2kda.import | 9.332 | 0.020 | 9.375 | |
| tool.aggregate | 0.002 | 0.000 | 0.001 | |
| tool.cluster | 0.021 | 0.000 | 0.021 | |
| tool.cluster.static | 0.000 | 0.000 | 0.001 | |
| tool.coalesce | 0.056 | 0.000 | 0.056 | |
| tool.coalesce.exec | 0.164 | 0.000 | 0.165 | |
| tool.coalesce.find | 0.169 | 0.000 | 0.169 | |
| tool.coalesce.merge | 0.168 | 0.000 | 0.168 | |
| tool.fdr | 0 | 0 | 0 | |
| tool.fdr.bh | 0 | 0 | 0 | |
| tool.fdr.empirical | 0.000 | 0.000 | 0.001 | |
| tool.graph | 1.320 | 0.008 | 1.331 | |
| tool.graph.degree | 1.488 | 0.004 | 1.496 | |
| tool.graph.list | 1.358 | 0.000 | 1.362 | |
| tool.metap | 0.003 | 0.000 | 0.004 | |
| tool.normalize | 0.014 | 0.000 | 0.015 | |
| tool.normalize.quality | 0.012 | 0.000 | 0.011 | |
| tool.overlap | 0.008 | 0.000 | 0.008 | |
| tool.read | 0.225 | 0.000 | 0.225 | |
| tool.save | 0.001 | 0.000 | 0.001 | |
| tool.subgraph | 0.072 | 0.000 | 0.072 | |
| tool.subgraph.find | 0.071 | 0.000 | 0.071 | |
| tool.subgraph.search | 0.071 | 0.000 | 0.072 | |
| tool.subgraph.stats | 0.083 | 0.004 | 0.087 | |
| tool.translate | 0.037 | 0.000 | 0.037 | |
| tool.unify | 0.001 | 0.000 | 0.001 | |