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This page was generated on 2024-03-28 11:32:16 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 99/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.12.0  (landing page)
Ariel Chernomoretz
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/ASpli
git_branch: RELEASE_3_18
git_last_commit: bf94d05
git_last_commit_date: 2023-10-24 10:51:51 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for ASpli on kjohnson1


To the developers/maintainers of the ASpli package:
- 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: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2024-03-27 05:35:57 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 05:56:55 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 1258.2 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_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ASpli.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.12.0’
* 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-3.18-bioc-mac-arm64/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 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 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           167.429  0.516 168.198
exportIntegratedSignals  87.425  0.300  87.855
integrateSignals         86.978  0.279  87.392
exportSplicingReports    86.312  0.268  86.691
splicingReport           85.308  0.243  85.749
jDUreport                84.268  0.270  85.010
jCounts-methods          84.275  0.238  84.638
gbCounts                 76.171  0.174  76.419
gbDUreport-method        75.054  0.211  75.385
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/Resources/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-package167.429 0.516168.198
DUreport000
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method0.0010.0000.000
acc_AS0.0000.0000.001
acc_DU0.0000.0000.001
acc_counts0.0000.0000.001
acc_features0.1920.0010.193
binGenome3.3760.0273.403
containsJunctions-function000
example_data000
exportIntegratedSignals87.425 0.30087.855
exportSplicingReports86.312 0.26886.691
filterDU-method0.0000.0010.001
filterSignals0.0000.0000.001
gbCounts76.171 0.17476.419
gbDUreport-method75.054 0.21175.385
getConditions-function0.0000.0010.000
integrateSignals86.978 0.27987.392
jCounts-methods84.275 0.23884.638
jDUreport84.268 0.27085.010
junctionDUreport000
loadBAM000
mergeBinDUAS-method0.0000.0010.001
plotBins0.0000.0010.000
plotGenomicRegions0.0000.0000.001
rds0.0000.0010.001
splicingReport85.308 0.24385.749
subset-methods0.0000.0010.001