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CHECK report for clipper on malbec2

This page was generated on 2019-04-09 11:34:24 -0400 (Tue, 09 Apr 2019).

Package 279/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.23.0
Paolo Martini
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/clipper
Branch: master
Last Commit: c41049a
Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: clipper
Version: 1.23.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clipper_1.23.0.tar.gz
StartedAt: 2019-04-08 23:29:54 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:42:14 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 740.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: clipper.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clipper_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/clipper.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.23.0’
* 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
clipperAllRoots      57.703  0.120  57.985
clipper              54.872  0.835  55.974
getGraphEntryGenes   47.028  0.035  49.344
easyClip             45.862  0.060  46.528
getJunctionTreePaths 45.666  0.055  48.191
cliqueMeanTest       43.753  0.064  44.132
cliqueVarianceTest   39.589  0.060  39.674
cliqueMixedTest      38.682  0.048  38.761
pathwayTest          38.216  0.048  38.264
cliquePairedTest     33.617  0.052  33.677
deleteEdge           30.254  0.048  30.314
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
  FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) : 
    Mean relative difference: 0.2461869
  
  
  Test files with failing tests
  
     test_clipper.R 
       test_clipper 
  
  
  Error in BiocGenerics:::testPackage("clipper") : 
    unit tests failed for package clipper
  Execution halted
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/clipper.Rcheck/00check.log’
for details.


Installation output

clipper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL clipper
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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.fail


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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'
Timing stopped at: 1.159 0 1.159
Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) : 
  Mean relative difference: 0.2461869



RUNIT TEST PROTOCOL -- Mon Apr  8 23:42:11 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
clipper RUnit Tests - 10 test functions, 0 errors, 1 failure
FAILURE in test_clipper: Error in checkEqualsNumeric(-log(0.001) * 2, as.numeric(clipped[1, 5])) : 
  Mean relative difference: 0.2461869


Test files with failing tests

   test_clipper.R 
     test_clipper 


Error in BiocGenerics:::testPackage("clipper") : 
  unit tests failed for package clipper
Execution halted

Example timings

clipper.Rcheck/clipper-Ex.timings

nameusersystemelapsed
clipper54.872 0.83555.974
clipperAllRoots57.703 0.12057.985
cliqueMeanTest43.753 0.06444.132
cliqueMixedTest38.682 0.04838.761
cliquePairedTest33.617 0.05233.677
cliqueVarianceTest39.589 0.06039.674
deleteEdge30.254 0.04830.314
easyClip45.862 0.06046.528
getGraphEntryGenes47.028 0.03549.344
getJunctionTreePaths45.666 0.05548.191
nameCliques0.0000.0000.001
pathwayTest38.216 0.04838.264
plotInCytoscape0.0010.0000.000
prunePaths0.0040.0000.003