Paolo Martini
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/clipper |
| Branch: RELEASE_3_10 |
| Last Commit: ae4ab82 |
| Last Changed Date: 2019-10-29 13:08:36 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:07:26 -0400 (Wed, 15 Apr 2020).
| Package 299/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clipper 1.26.0 Paolo Martini
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: clipper |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings clipper_1.26.0.tar.gz |
| StartedAt: 2020-04-15 01:34:13 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:39:38 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 325.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clipper.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:clipper.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings clipper_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/clipper.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.26.0’
* 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 13.740 0.132 13.968
pathwayTest 8.416 0.008 8.443
clipper 7.604 0.124 7.864
cliqueMixedTest 4.964 0.028 5.031
* 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: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL clipper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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)
clipper.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 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 Apr 15 01:39:34 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
16.872 0.528 17.582
clipper.Rcheck/clipper-Ex.timings
| name | user | system | elapsed | |
| clipper | 7.604 | 0.124 | 7.864 | |
| clipperAllRoots | 13.740 | 0.132 | 13.968 | |
| cliqueMeanTest | 4.048 | 0.028 | 4.141 | |
| cliqueMixedTest | 4.964 | 0.028 | 5.031 | |
| cliquePairedTest | 4.272 | 0.020 | 4.307 | |
| cliqueVarianceTest | 4.932 | 0.044 | 4.996 | |
| deleteEdge | 1.220 | 0.004 | 1.230 | |
| easyClip | 4.100 | 0.036 | 4.158 | |
| getGraphEntryGenes | 1.068 | 0.000 | 1.072 | |
| getJunctionTreePaths | 1.188 | 0.004 | 1.196 | |
| nameCliques | 0.000 | 0.000 | 0.001 | |
| pathwayTest | 8.416 | 0.008 | 8.443 | |
| plotInCytoscape | 0 | 0 | 0 | |
| prunePaths | 0.004 | 0.000 | 0.005 | |