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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1292/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff2 1.34.0  (landing page)
Gabriele Schweikert
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/MMDiff2
git_branch: RELEASE_3_20
git_last_commit: d181cca
git_last_commit_date: 2024-10-29 10:10:51 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MMDiff2 on kunpeng2

To the developers/maintainers of the MMDiff2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MMDiff2.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: MMDiff2
Version: 1.34.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MMDiff2_1.34.0.tar.gz
StartedAt: 2024-11-20 09:59:54 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:06:53 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 419.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MMDiff2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MMDiff2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MMDiff2_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MMDiff2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMDiff2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff2’ version ‘1.34.0’
* 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 ‘MMDiff2’ 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 ... 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DBAmmd: no visible global function definition for ‘new’
getReads: no visible global function definition for ‘IRangesList’
Undefined global functions or variables:
  IRangesList new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) DBAmmd-class.Rd:20: Lost braces
    20 | \code{DBAmmd()}{returns an empty DBAmmd Object.} \cr
       |                ^
checkRd: (-1) DBAmmd-class.Rd:21-23: Lost braces
    21 | \code{DBAmmd(MetaData)}{ initializes a DBAmmd Object for a new
       |                        ^
* 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
compDists        60.133  0.631  60.718
DBAmmd-Accessors 15.237  0.203  15.518
plotPeak          7.069  0.060   7.142
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MMDiff2.Rcheck/00check.log’
for details.


Installation output

MMDiff2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MMDiff2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘MMDiff2’ ...
** using staged installation
** R
** data
** 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 (MMDiff2)

Tests output


Example timings

MMDiff2.Rcheck/MMDiff2-Ex.timings

nameusersystemelapsed
Cfp1-Peaks0.0000.0000.001
DBAmmd-Accessors15.237 0.20315.518
DBAmmd-class0.0430.0080.052
MMD000
compDists60.133 0.63160.718
compHists4.4160.1684.590
compPvals1.2670.0361.304
estimateFragmentCenters1.5340.0351.573
getPeakReads0.3310.0010.357
mm9-Genes000
plotDISTS4Peak1.1540.0351.192
plotDists1.1330.0361.171
plotPeak7.0690.0607.142
reportResults1.2660.0361.305
runShinyMMDiff20.0000.0000.001
server.MMDiff20.0010.0000.000
ui.MMDiff2000