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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 100/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.15.0  (landing page)
Ariel Chernomoretz
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/ASpli
git_branch: devel
git_last_commit: c7e1da6
git_last_commit_date: 2024-04-30 10:52:43 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for ASpli on palomino4

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: 2.15.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASpli.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ASpli_2.15.0.tar.gz
StartedAt: 2024-06-09 23:42:22 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-10 00:02:49 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 1226.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ASpli.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASpli.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ASpli_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ASpli.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ASpli/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASpli' version '2.15.0'
* 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 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 'F:/biocbuild/bbs-3.20-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 ... 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 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           131.59   0.81  133.13
exportIntegratedSignals  71.00   1.00   73.62
exportSplicingReports    70.36   0.86   71.28
integrateSignals         69.67   0.62   70.39
splicingReport           68.50   0.64   69.15
jCounts-methods          67.89   0.58   68.47
jDUreport                67.35   0.63   68.00
gbCounts                 62.89   0.59   63.48
gbDUreport-method        61.30   0.66   61.97
* 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, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ASpli.Rcheck/00check.log'
for details.


Installation output

ASpli.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ASpli
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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-package131.59 0.81133.13
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method000
acc_AS000
acc_DU000
acc_counts0.010.000.02
acc_features0.250.000.25
binGenome3.740.634.39
containsJunctions-function000
example_data000
exportIntegratedSignals71.00 1.0073.62
exportSplicingReports70.36 0.8671.28
filterDU-method000
filterSignals000
gbCounts62.89 0.5963.48
gbDUreport-method61.30 0.6661.97
getConditions-function000
integrateSignals69.67 0.6270.39
jCounts-methods67.89 0.5868.47
jDUreport67.35 0.6368.00
junctionDUreport000
loadBAM000
mergeBinDUAS-method000
plotBins000
plotGenomicRegions000
rds000
splicingReport68.50 0.6469.15
subset-methods000