Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:05:55 -0400 (Sat, 23 Oct 2021).

CHECK results for clipper on nebbiolo2

To the developers/maintainers of the clipper package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clipper.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 328/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.33.0  (landing page)
Paolo Martini
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/clipper
git_branch: master
git_last_commit: 2b5f6b6
git_last_commit_date: 2021-05-19 11:57:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: clipper
Version: 1.33.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings clipper_1.33.0.tar.gz
StartedAt: 2021-10-22 19:31:09 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 19:35:53 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 284.1 seconds
RetCode: 0
Status:   OK  
CheckDir: clipper.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings clipper_1.33.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/clipper.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.33.0’
* 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 ‘clipper’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
clipperAllRoots 9.613  0.232   9.845
clipper         6.305  0.159   6.465
pathwayTest     5.066  0.064   5.130
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: OK


Installation output

clipper.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL clipper
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘clipper’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
** testing if installed package can be loaded from final location
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
** testing if installed package keeps a record of temporary installation path
* DONE (clipper)

Tests output

clipper.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("clipper")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'


RUNIT TEST PROTOCOL -- Fri Oct 22 19:35:50 2021 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
clipper RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> pattern="^test_.*\\.R$"
> 
> proc.time()
   user  system elapsed 
 13.971   0.647  14.604 

Example timings

clipper.Rcheck/clipper-Ex.timings

nameusersystemelapsed
clipper6.3050.1596.465
clipperAllRoots9.6130.2329.845
cliqueMeanTest2.8730.0762.950
cliqueMixedTest3.9040.0723.975
cliquePairedTest3.3330.0763.409
cliqueVarianceTest2.7930.0602.853
deleteEdge0.8340.0040.837
easyClip2.7960.0722.869
getGraphEntryGenes0.9630.0160.979
getJunctionTreePaths0.970.020.99
nameCliques0.0010.0000.001
pathwayTest5.0660.0645.130
plotInCytoscape000
prunePaths0.0040.0000.004