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CHECK report for clipper on malbec1

This page was generated on 2019-04-16 11:49:53 -0400 (Tue, 16 Apr 2019).

Package 270/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.22.0
Paolo Martini
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/clipper
Branch: RELEASE_3_8
Last Commit: e798b1c
Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clipper
Version: 1.22.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings clipper_1.22.0.tar.gz
StartedAt: 2019-04-15 22:57:15 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:09:36 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 741.2 seconds
RetCode: 0
Status:  OK 
CheckDir: clipper.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings clipper_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/clipper.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.22.0’
* 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 or elapsed time > 5s
                       user system elapsed
clipper              53.744  0.692  54.801
clipperAllRoots      51.444  0.040  51.598
getJunctionTreePaths 49.652  0.008  51.579
getGraphEntryGenes   47.608  0.012  51.000
pathwayTest          45.356  0.064  45.552
cliqueMixedTest      45.068  0.092  45.251
cliqueMeanTest       44.012  0.080  44.236
cliquePairedTest     43.544  0.032  43.619
easyClip             43.388  0.076  43.654
cliqueVarianceTest   39.256  0.056  39.349
deleteEdge           29.248  0.024  29.311
* 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-3.8-bioc/R/bin/R CMD INSTALL clipper
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘clipper’ ...
** 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
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
* DONE (clipper)

Tests output

clipper.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    colMeans, colSums, rowMeans, rowSums, which

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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


RUNIT TEST PROTOCOL -- Mon Apr 15 23:09:33 2019 
*********************************************** 
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 
 14.484   0.520  15.037 

Example timings

clipper.Rcheck/clipper-Ex.timings

nameusersystemelapsed
clipper53.744 0.69254.801
clipperAllRoots51.444 0.04051.598
cliqueMeanTest44.012 0.08044.236
cliqueMixedTest45.068 0.09245.251
cliquePairedTest43.544 0.03243.619
cliqueVarianceTest39.256 0.05639.349
deleteEdge29.248 0.02429.311
easyClip43.388 0.07643.654
getGraphEntryGenes47.608 0.01251.000
getJunctionTreePaths49.652 0.00851.579
nameCliques000
pathwayTest45.356 0.06445.552
plotInCytoscape000
prunePaths0.0040.0000.006