Paolo Martini
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/clipper |
| Branch: master |
| Last Commit: e2f3341 |
| Last Changed Date: 2019-10-29 13:36:30 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:36:17 -0500 (Thu, 16 Jan 2020).
| Package 299/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clipper 1.27.0 Paolo Martini
| malbec2 | Linux (Ubuntu 18.04.3 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: 1.27.0 |
| 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_1.27.0.tar.gz |
| StartedAt: 2020-01-16 02:56:24 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:05:19 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 535.4 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_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/clipper.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.27.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
clipperAllRoots 22.656 1.019 24.349
clipper 9.887 0.560 12.330
pathwayTest 8.050 0.088 8.195
cliqueMixedTest 6.149 0.185 6.378
cliquePairedTest 5.190 0.116 5.318
cliqueMeanTest 5.069 0.104 5.255
cliqueVarianceTest 4.949 0.098 5.090
* 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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 -- Thu Jan 16 03:05:07 2020
***********************************************
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
25.521 1.826 28.652
clipper.Rcheck/clipper-Ex.timings
| name | user | system | elapsed | |
| clipper | 9.887 | 0.560 | 12.330 | |
| clipperAllRoots | 22.656 | 1.019 | 24.349 | |
| cliqueMeanTest | 5.069 | 0.104 | 5.255 | |
| cliqueMixedTest | 6.149 | 0.185 | 6.378 | |
| cliquePairedTest | 5.190 | 0.116 | 5.318 | |
| cliqueVarianceTest | 4.949 | 0.098 | 5.090 | |
| deleteEdge | 1.219 | 0.013 | 1.258 | |
| easyClip | 4.172 | 0.093 | 4.344 | |
| getGraphEntryGenes | 1.321 | 0.015 | 1.382 | |
| getJunctionTreePaths | 1.357 | 0.020 | 1.382 | |
| nameCliques | 0.000 | 0.000 | 0.001 | |
| pathwayTest | 8.050 | 0.088 | 8.195 | |
| plotInCytoscape | 0.000 | 0.001 | 0.001 | |
| prunePaths | 0.008 | 0.002 | 0.009 | |