Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-07-24 12:05:22 -0400 (Sat, 24 Jul 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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 313/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.33.0  (landing page)
Paolo Martini
Snapshot Date: 2021-07-23 14:50:08 -0400 (Fri, 23 Jul 2021)
URL: https://git.bioconductor.org/packages/clipper
Branch: master
Last Commit: 2b5f6b6
Last Changed 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  NO, package depends on 'qpgraph' which is not available
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: 2021-07-23 19:09:27 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 19:14:31 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 304.9 seconds
RetCode: 0
Status:   OK  
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/clipper.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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
clipper         8.967  0.439   9.410
clipperAllRoots 8.223  0.088   8.312
pathwayTest     4.964  0.056   5.020
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL clipper
###
##############################################################################
##############################################################################


* 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 4.1.0 beta (2021-05-03 r80259) -- "Camp Pontanezen"
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 Jul 23 19:14:29 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 
 13.371   0.556  13.914 

Example timings

clipper.Rcheck/clipper-Ex.timings

nameusersystemelapsed
clipper8.9670.4399.410
clipperAllRoots8.2230.0888.312
cliqueMeanTest3.9720.3124.284
cliqueMixedTest2.7220.0322.754
cliquePairedTest3.6840.1683.852
cliqueVarianceTest2.6060.0242.630
deleteEdge0.8680.0040.873
easyClip2.6940.1122.806
getGraphEntryGenes0.9310.0280.959
getJunctionTreePaths0.8510.0040.856
nameCliques0.0000.0000.001
pathwayTest4.9640.0565.020
plotInCytoscape0.0010.0000.000
prunePaths0.0040.0000.003