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This page was generated on 2025-02-26 11:45 -0500 (Wed, 26 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4663
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4493
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4504
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4458
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4313
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 104/2302HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.17.0  (landing page)
Ariel Chernomoretz
Snapshot Date: 2025-02-25 13:40 -0500 (Tue, 25 Feb 2025)
git_url: https://git.bioconductor.org/packages/ASpli
git_branch: devel
git_last_commit: 5b28a12
git_last_commit_date: 2024-10-29 10:12:56 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for ASpli on kjohnson3

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

raw results


Summary

Package: ASpli
Version: 2.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASpli_2.17.0.tar.gz
StartedAt: 2025-02-25 18:44:18 -0500 (Tue, 25 Feb 2025)
EndedAt: 2025-02-25 18:51:38 -0500 (Tue, 25 Feb 2025)
EllapsedTime: 439.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ASpli.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ASpli_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ASpli.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.17.0’
* 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 ‘ASpli’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ASpli.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'txdbmaker'
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DUreport.Rd: edgeR
  DUreport.norm.Rd: edgeR
  DUreport.offset.Rd: edgeR
  DUreportBinSplice-method.Rd: edgeR
  gbDUreport-method.Rd: edgeR
  jDUreport.Rd: edgeR
  junctionDUreport.Rd: edgeR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
ASpli-package           61.944  0.323  61.037
exportIntegratedSignals 32.055  0.207  32.743
exportSplicingReports   31.836  0.186  31.787
integrateSignals        31.223  0.209  31.078
splicingReport          31.001  0.266  30.590
jDUreport               30.703  0.203  30.112
jCounts-methods         30.607  0.186  30.386
gbCounts                28.401  0.146  28.395
gbDUreport-method       27.528  0.193  26.934
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ASpli.Rcheck/00check.log’
for details.


Installation output

ASpli.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ASpli
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ASpli’ ...
** this is package ‘ASpli’ version ‘2.17.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’
** testing if installed package keeps a record of temporary installation path
* DONE (ASpli)

Tests output


Example timings

ASpli.Rcheck/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package61.944 0.32361.037
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method000
acc_AS000
acc_DU000
acc_counts000
acc_features0.0530.0000.054
binGenome0.9650.0061.007
containsJunctions-function000
example_data000
exportIntegratedSignals32.055 0.20732.743
exportSplicingReports31.836 0.18631.787
filterDU-method000
filterSignals000
gbCounts28.401 0.14628.395
gbDUreport-method27.528 0.19326.934
getConditions-function000
integrateSignals31.223 0.20931.078
jCounts-methods30.607 0.18630.386
jDUreport30.703 0.20330.112
junctionDUreport0.0010.0000.000
loadBAM000
mergeBinDUAS-method0.0000.0000.001
plotBins0.0000.0010.000
plotGenomicRegions0.0000.0000.001
rds000
splicingReport31.001 0.26630.590
subset-methods0.0000.0000.001