Paolo Martini
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/clipper |
| Branch: RELEASE_3_7 |
| Last Commit: ef0a6fe |
| Last Changed Date: 2018-05-02 09:56:36 -0400 (Wed, 02 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:51:12 -0400 (Wed, 17 Oct 2018).
| Package 254/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clipper 1.20.1 Paolo Martini
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: clipper |
| Version: 1.20.1 |
| 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_1.20.1.tar.gz |
| StartedAt: 2018-10-16 20:30:33 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:35:55 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 322.5 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_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/clipper.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.20.1’
* 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 15.931 1.853 17.967
clipperAllRoots 15.063 0.544 15.782
pathwayTest 6.928 0.099 7.088
* 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/3.5/Resources/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)
clipper.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 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 -- Tue Oct 16 20:35:49 2018
***********************************************
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
14.076 0.728 14.916
clipper.Rcheck/clipper-Ex.timings
| name | user | system | elapsed | |
| clipper | 15.931 | 1.853 | 17.967 | |
| clipperAllRoots | 15.063 | 0.544 | 15.782 | |
| cliqueMeanTest | 3.868 | 0.116 | 4.030 | |
| cliqueMixedTest | 3.802 | 0.083 | 3.922 | |
| cliquePairedTest | 3.871 | 0.066 | 3.978 | |
| cliqueVarianceTest | 3.282 | 0.078 | 3.392 | |
| deleteEdge | 0.623 | 0.006 | 0.635 | |
| easyClip | 3.344 | 0.047 | 3.439 | |
| getGraphEntryGenes | 0.654 | 0.010 | 0.669 | |
| getJunctionTreePaths | 0.680 | 0.011 | 0.697 | |
| nameCliques | 0.002 | 0.000 | 0.003 | |
| pathwayTest | 6.928 | 0.099 | 7.088 | |
| plotInCytoscape | 0.002 | 0.000 | 0.003 | |
| prunePaths | 0.008 | 0.001 | 0.008 | |