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This page was generated on 2021-09-20 15:05:35 -0400 (Mon, 20 Sep 2021).

CHECK results for ASpli on machv2

To the developers/maintainers of the ASpli package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 94/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASpli 2.2.0  (landing page)
Estefania Mancini
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/ASpli
git_branch: RELEASE_3_13
git_last_commit: 6dddfb0
git_last_commit_date: 2021-05-19 12:22:07 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ASpli
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASpli_2.2.0.tar.gz
StartedAt: 2021-09-19 16:17:49 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 16:36:21 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 1112.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ASpli.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASpli.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASpli_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ASpli.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ASpli/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ASpli’ version ‘2.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ASpli’ 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 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           137.121  0.497 137.758
exportIntegratedSignals  74.366  0.244  74.691
integrateSignals         72.518  0.146  72.735
exportSplicingReports    71.585  0.286  71.933
jDUreport                71.510  0.148  71.738
splicingReport           70.838  0.150  71.074
jCounts-methods          69.248  0.195  69.521
gbCounts                 61.894  0.100  62.041
gbDUreport-method        61.027  0.143  61.245
binGenome                 7.168  0.041   7.212
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ASpli.Rcheck/00check.log’
for details.



Installation output

ASpli.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ASpli’ ...
** using staged installation
** R
** inst
** 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 (ASpli)

Tests output


Example timings

ASpli.Rcheck/ASpli-Ex.timings

nameusersystemelapsed
ASpli-package137.121 0.497137.758
DUreport0.0000.0000.001
DUreport.norm000
DUreport.offset000
DUreportBinSplice-method0.0010.0010.001
acc_AS0.0010.0010.001
acc_DU0.0000.0010.001
acc_counts0.0000.0000.001
acc_features0.4500.0010.452
binGenome7.1680.0417.212
containsJunctions-function0.0010.0000.001
example_data0.0000.0000.001
exportIntegratedSignals74.366 0.24474.691
exportSplicingReports71.585 0.28671.933
filterDU-method0.0010.0010.001
filterSignals0.0010.0000.001
gbCounts61.894 0.10062.041
gbDUreport-method61.027 0.14361.245
getConditions-function0.0010.0000.001
integrateSignals72.518 0.14672.735
jCounts-methods69.248 0.19569.521
jDUreport71.510 0.14871.738
junctionDUreport0.0000.0010.000
loadBAM000
mergeBinDUAS-method0.0000.0000.001
plotBins0.0000.0010.001
plotGenomicRegions0.0000.0010.001
rds0.0000.0010.001
splicingReport70.838 0.15071.074
subset-methods0.0010.0010.002