Taosheng Xu
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CancerSubtypes |
| Branch: RELEASE_3_7 |
| Last Commit: 45e20fe |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:29:18 -0400 (Wed, 17 Oct 2018).
| Package 186/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CancerSubtypes 1.6.0 Taosheng Xu
| 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: CancerSubtypes |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CancerSubtypes_1.6.0.tar.gz |
| StartedAt: 2018-10-15 22:58:32 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:00:58 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 146.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CancerSubtypes.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CancerSubtypes_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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
ExecuteCNMF 37.900 1.472 11.711
sigclustTest 23.356 0.020 23.401
ExecuteSNF.CC 14.468 0.096 14.610
survAnalysis 8.456 0.020 8.482
ExecuteCC 6.732 0.032 6.771
* 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: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CancerSubtypes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘CancerSubtypes’ ... ** 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 * DONE (CancerSubtypes)
CancerSubtypes.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-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("CancerSubtypes")
Attaching package: 'pkgmaker'
The following object is masked from 'package:base':
isFALSE
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 19/20
To enable shared memory capabilities, try: install.extras('
NMF
')
RUNIT TEST PROTOCOL -- Mon Oct 15 23:00:56 2018
***********************************************
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
3.200 0.144 3.510
CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings
| name | user | system | elapsed | |
| DiffExp.limma | 0.284 | 0.028 | 0.310 | |
| ExecuteCC | 6.732 | 0.032 | 6.771 | |
| ExecuteCNMF | 37.900 | 1.472 | 11.711 | |
| ExecuteSNF.CC | 14.468 | 0.096 | 14.610 | |
| ExecuteSNF | 0.22 | 0.00 | 0.22 | |
| ExecuteWSNF | 1.612 | 0.016 | 1.630 | |
| ExecuteiCluster | 3.292 | 0.004 | 3.296 | |
| FSbyCox | 4.840 | 0.000 | 4.845 | |
| FSbyMAD | 0.216 | 0.000 | 0.217 | |
| FSbyPCA | 0.132 | 0.000 | 0.135 | |
| FSbyVar | 0.128 | 0.000 | 0.129 | |
| GeneExp | 0.040 | 0.000 | 0.042 | |
| Ranking | 0.028 | 0.000 | 0.028 | |
| data.checkDistribution | 0.34 | 0.00 | 0.34 | |
| data.imputation | 0.008 | 0.000 | 0.007 | |
| data.normalization | 0.12 | 0.00 | 0.12 | |
| drawHeatmap | 4.208 | 0.036 | 4.269 | |
| miRNAExp | 0.008 | 0.000 | 0.006 | |
| saveFigure | 0.880 | 0.016 | 0.899 | |
| sigclustTest | 23.356 | 0.020 | 23.401 | |
| silhouette_SimilarityMatrix | 0.252 | 0.000 | 0.251 | |
| spectralAlg | 0.028 | 0.000 | 0.029 | |
| status | 0.004 | 0.000 | 0.001 | |
| survAnalysis | 8.456 | 0.020 | 8.482 | |
| time | 0.004 | 0.000 | 0.002 | |