Paolo Martini
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/clipper |
| Branch: RELEASE_3_9 |
| Last Commit: d689548 |
| Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:51:00 -0400 (Wed, 16 Oct 2019).
| Package 284/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clipper 1.24.0 Paolo Martini
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: clipper |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clipper_1.24.0.tar.gz |
| StartedAt: 2019-10-16 01:31:34 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:47:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 936.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clipper.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clipper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clipper_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/clipper.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.24.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipper 64.145 3.395 67.901
clipperAllRoots 65.962 1.307 68.322
cliqueMeanTest 51.454 1.639 53.807
cliqueMixedTest 50.547 0.921 52.558
pathwayTest 49.904 1.293 53.085
cliquePairedTest 49.376 0.781 50.236
getGraphEntryGenes 45.290 1.243 49.518
getJunctionTreePaths 44.273 1.115 50.375
easyClip 43.487 0.441 43.990
cliqueVarianceTest 43.072 0.535 43.617
deleteEdge 40.504 0.349 40.859
* 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
clipper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clipper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)
clipper.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 object is masked from 'package:Matrix':
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, 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, which.max, which.min
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
RUNIT TEST PROTOCOL -- Wed Oct 16 01:47:03 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
18.289 1.520 19.765
clipper.Rcheck/clipper-Ex.timings
| name | user | system | elapsed | |
| clipper | 64.145 | 3.395 | 67.901 | |
| clipperAllRoots | 65.962 | 1.307 | 68.322 | |
| cliqueMeanTest | 51.454 | 1.639 | 53.807 | |
| cliqueMixedTest | 50.547 | 0.921 | 52.558 | |
| cliquePairedTest | 49.376 | 0.781 | 50.236 | |
| cliqueVarianceTest | 43.072 | 0.535 | 43.617 | |
| deleteEdge | 40.504 | 0.349 | 40.859 | |
| easyClip | 43.487 | 0.441 | 43.990 | |
| getGraphEntryGenes | 45.290 | 1.243 | 49.518 | |
| getJunctionTreePaths | 44.273 | 1.115 | 50.375 | |
| nameCliques | 0.001 | 0.000 | 0.002 | |
| pathwayTest | 49.904 | 1.293 | 53.085 | |
| plotInCytoscape | 0 | 0 | 0 | |
| prunePaths | 0.005 | 0.001 | 0.005 | |