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 12:09:28 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CancerSubtypes_1.10.0.tar.gz |
| StartedAt: 2019-10-16 00:16:23 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:19:53 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 210.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CancerSubtypes.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CancerSubtypes_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.0’
* 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
ExecuteCNMF 44.456 2.206 14.270
sigclustTest 37.248 0.026 37.285
ExecuteSNF.CC 20.453 0.100 20.559
survAnalysis 15.084 0.008 15.095
FSbyCox 8.929 0.000 8.935
ExecuteCC 8.165 0.036 8.207
* 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-3.9-bioc/R/bin/R CMD INSTALL CancerSubtypes ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-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 -- Wed Oct 16 00:19:49 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
3.152 0.180 3.344
CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings
| name | user | system | elapsed | |
| DiffExp.limma | 0.462 | 0.016 | 0.477 | |
| ExecuteCC | 8.165 | 0.036 | 8.207 | |
| ExecuteCNMF | 44.456 | 2.206 | 14.270 | |
| ExecuteSNF.CC | 20.453 | 0.100 | 20.559 | |
| ExecuteSNF | 0.363 | 0.004 | 0.366 | |
| ExecuteWSNF | 2.433 | 0.016 | 2.450 | |
| ExecuteiCluster | 3.379 | 0.004 | 3.383 | |
| FSbyCox | 8.929 | 0.000 | 8.935 | |
| FSbyMAD | 0.311 | 0.000 | 0.310 | |
| FSbyPCA | 0.158 | 0.000 | 0.158 | |
| FSbyVar | 0.128 | 0.004 | 0.131 | |
| GeneExp | 0.062 | 0.004 | 0.066 | |
| Ranking | 0.047 | 0.000 | 0.047 | |
| data.checkDistribution | 0.44 | 0.00 | 0.44 | |
| data.imputation | 0.007 | 0.000 | 0.007 | |
| data.normalization | 0.127 | 0.000 | 0.128 | |
| drawHeatmap | 4.382 | 0.036 | 4.418 | |
| miRNAExp | 0.005 | 0.000 | 0.004 | |
| saveFigure | 1.086 | 0.013 | 1.099 | |
| sigclustTest | 37.248 | 0.026 | 37.285 | |
| silhouette_SimilarityMatrix | 0.464 | 0.003 | 0.467 | |
| spectralAlg | 0.025 | 0.000 | 0.027 | |
| status | 0.001 | 0.000 | 0.001 | |
| survAnalysis | 15.084 | 0.008 | 15.095 | |
| time | 0.000 | 0.002 | 0.002 | |