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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 520/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DegCre 1.3.0  (landing page)
Brian S. Roberts
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/DegCre
git_branch: devel
git_last_commit: 0bf1459
git_last_commit_date: 2024-12-13 16:10:45 -0500 (Fri, 13 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'plotgardener' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for DegCre on kunpeng2

To the developers/maintainers of the DegCre package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DegCre.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.

raw results


Summary

Package: DegCre
Version: 1.3.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DegCre.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DegCre_1.3.0.tar.gz
StartedAt: 2024-12-24 05:58:30 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 06:07:32 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 542.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DegCre.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DegCre.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DegCre_1.3.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DegCre.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘DegCre/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DegCre’ version ‘1.3.0’
* package encoding: UTF-8
* 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 ‘DegCre’ can be installed ... OK
* checking installed package size ... OK
* 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 ...Warning: program compiled against libxml 212 using older 211
 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
calcPadjsAndEtpFun: multiple local function definitions for ‘tpFun’
  with different formal arguments
* 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
degCrePRAUC              19.280  0.051  19.369
optimizeAlphaDegCre      12.641  0.060  12.727
plotBrowserDegCre        12.096  0.092  12.459
getExpectAssocPerDEG      6.519  0.044   6.578
plotExpectedAssocsPerDeg  6.322  0.060   6.395
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.21-bioc/meat/DegCre.Rcheck/00check.log’
for details.


Installation output

DegCre.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DegCre
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘DegCre’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (DegCre)

Tests output

DegCre.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(DegCre)

> 
> test_check("DegCre")
Processing 23235 associations for gene collapse
Using GeneSymb as gene name column.
Minimum display region size = 29091 bp.
All smaller regions will be expanded.
ACOT7 promoters have been merged for plotting.
HES2 promoters have been merged for plotting.
ERRFI1 promoters have been merged for plotting.
SLC2A5 promoters have been merged for plotting.
GPR157 promoters have been merged for plotting.
SPSB1 promoters have been merged for plotting.
arches[arches1]
heatmapLegend[heatmapLegend1]
signal[signal1_h]
yaxis[yaxis1]
genomeLabel[genomeLabel1]
genes[genes1]
genes[genes2]
text[text1]
text[text2]
text[text2]
Analyzing 34169 DegGR to CreGR hits for optimal distance bin size.
Hit distance bin n = 2277
Small last bin resolved.
Running over 16 hit distance thresholds
Adjusting association probability for distance.
Calculation of assoc probabilities over hit bins complete.
Assoc FDR calculation complete.
DegCre calculations complete.
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 91.521   1.429  93.194 

Example timings

DegCre.Rcheck/DegCre-Ex.timings

nameusersystemelapsed
adjustRawAssocProb000
calcAUC000
calcAssocProbOR3.9860.0964.089
calcBinomFDRperBin000
calcDependIndependEnrichStats0.0010.0000.000
calcKStestStatMedian000
calcPadjsAndEtpFun000
calcRawAssocProbOR2.7080.0162.729
changeColorAlpha0.0000.0000.001
collapseDegCreToGene3.7620.1123.881
convDegCreResListToCreGeneScoreGR2.6870.0162.708
convertDegCreDataFrame2.7260.0112.744
convertdegCreResListToGInteraction2.7830.0002.789
correctAssocProbs000
creGRToSignal000
degCrePRAUC19.280 0.05119.369
distBinHeuristic000
fastKS000
getAssocDistHits3.9240.1004.032
getDegCrePlotRegionFromGene000
getDistBinNullAssocProb3.6900.0483.746
getExpectAssocPerDEG6.5190.0446.578
getLabelYfromPlotgardenerObj0.0010.0000.000
makeDistBinChunkList000
makePlotGInter000
optimizeAlphaDegCre12.641 0.06012.727
plotBrowserDegCre12.096 0.09212.459
plotDegCreAssocProbVsDist2.6110.0122.629
plotDegCreBinHeuristic2.5500.0042.559
plotExpectedAssocsPerDeg6.3220.0606.395
runDegCre3.2050.0123.224