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This page was generated on 2024-02-26 13:58:15 -0500 (Mon, 26 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 100/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.13.0  (landing page)
Ariel Chernomoretz
Snapshot Date: 2024-02-23 14:00:08 -0500 (Fri, 23 Feb 2024)
git_url: https://git.bioconductor.org/packages/ASpli
git_branch: devel
git_last_commit: 7525b85
git_last_commit_date: 2023-10-24 10:51:51 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for ASpli on nebbiolo1


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: 2.13.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ASpli_2.13.0.tar.gz
StartedAt: 2024-02-23 20:11:19 -0500 (Fri, 23 Feb 2024)
EndedAt: 2024-02-23 20:28:41 -0500 (Fri, 23 Feb 2024)
EllapsedTime: 1041.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ASpli.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ASpli.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ASpli_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ASpli.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.13.0’
* 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 ‘/home/biocbuild/bbs-3.19-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 R 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 ... OK
* 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 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           120.682  1.436 121.907
exportSplicingReports    63.614  2.816  66.327
exportIntegratedSignals  64.460  0.350  64.687
integrateSignals         62.153  0.464  62.498
jCounts-methods          62.059  0.344  62.293
splicingReport           61.558  0.309  61.759
jDUreport                60.897  0.303  61.098
gbDUreport-method        54.135  0.457  54.485
gbCounts                 53.713  0.747  54.348
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ASpli.Rcheck/00check.log’
for details.



Installation output

ASpli.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ASpli
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘ASpli’ ...
** 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-package120.682 1.436121.907
DUreport000
DUreport.norm0.0000.0000.001
DUreport.offset000
DUreportBinSplice-method000
acc_AS0.0000.0010.001
acc_DU000
acc_counts000
acc_features0.1500.0030.154
binGenome3.2220.0043.226
containsJunctions-function000
example_data0.0000.0000.001
exportIntegratedSignals64.460 0.35064.687
exportSplicingReports63.614 2.81666.327
filterDU-method000
filterSignals000
gbCounts53.713 0.74754.348
gbDUreport-method54.135 0.45754.485
getConditions-function000
integrateSignals62.153 0.46462.498
jCounts-methods62.059 0.34462.293
jDUreport60.897 0.30361.098
junctionDUreport000
loadBAM0.0000.0000.001
mergeBinDUAS-method0.0010.0000.001
plotBins0.0010.0000.001
plotGenomicRegions000
rds000
splicingReport61.558 0.30961.759
subset-methods000