Taosheng Xu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CancerSubtypes |
| Branch: RELEASE_3_9 |
| Last Commit: a2147f9 |
| Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:58:34 -0400 (Wed, 16 Oct 2019).
| Package 209/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CancerSubtypes 1.10.0 Taosheng Xu
| 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: CancerSubtypes |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerSubtypes_1.10.0.tar.gz |
| StartedAt: 2019-10-16 01:08:51 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:14:14 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 323.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CancerSubtypes.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerSubtypes_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CancerSubtypes.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 ‘CancerSubtypes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CancerSubtypes’ version ‘1.10.0’
* 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 ‘CancerSubtypes’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigclustTest 49.463 13.766 63.373
ExecuteCNMF 50.469 7.882 17.823
ExecuteSNF.CC 27.547 2.482 30.082
survAnalysis 21.344 0.437 21.846
ExecuteCC 13.940 3.100 17.056
FSbyCox 13.817 0.249 14.069
drawHeatmap 7.392 0.257 7.684
ExecuteiCluster 5.511 0.138 5.646
* 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
CancerSubtypes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CancerSubtypes ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘CancerSubtypes’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CancerSubtypes)
CancerSubtypes.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("CancerSubtypes")
Attaching package: 'pkgmaker'
The following object is masked from 'package:base':
isFALSE
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 22/23
To enable shared memory capabilities, try: install.extras('
NMF
')
RUNIT TEST PROTOCOL -- Wed Oct 16 01:14:06 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
CancerSubtypes RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.134 0.560 5.654
CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings
| name | user | system | elapsed | |
| DiffExp.limma | 0.563 | 0.121 | 0.683 | |
| ExecuteCC | 13.940 | 3.100 | 17.056 | |
| ExecuteCNMF | 50.469 | 7.882 | 17.823 | |
| ExecuteSNF.CC | 27.547 | 2.482 | 30.082 | |
| ExecuteSNF | 0.267 | 0.038 | 0.304 | |
| ExecuteWSNF | 3.210 | 0.119 | 3.384 | |
| ExecuteiCluster | 5.511 | 0.138 | 5.646 | |
| FSbyCox | 13.817 | 0.249 | 14.069 | |
| FSbyMAD | 0.485 | 0.021 | 0.507 | |
| FSbyPCA | 0.236 | 0.033 | 0.269 | |
| FSbyVar | 0.160 | 0.033 | 0.192 | |
| GeneExp | 0.058 | 0.011 | 0.069 | |
| Ranking | 0.032 | 0.005 | 0.036 | |
| data.checkDistribution | 0.417 | 0.031 | 0.448 | |
| data.imputation | 0.015 | 0.001 | 0.015 | |
| data.normalization | 0.226 | 0.012 | 0.237 | |
| drawHeatmap | 7.392 | 0.257 | 7.684 | |
| miRNAExp | 0.006 | 0.003 | 0.010 | |
| saveFigure | 1.604 | 0.125 | 1.749 | |
| sigclustTest | 49.463 | 13.766 | 63.373 | |
| silhouette_SimilarityMatrix | 0.731 | 0.057 | 0.788 | |
| spectralAlg | 0.047 | 0.005 | 0.053 | |
| status | 0.002 | 0.004 | 0.006 | |
| survAnalysis | 21.344 | 0.437 | 21.846 | |
| time | 0.002 | 0.013 | 0.015 | |