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BioC 3.2: CHECK report for RTN on oaxaca

This page was generated on 2015-10-27 17:40:47 -0400 (Tue, 27 Oct 2015).

Package 925/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTN 1.8.0
Mauro Castro
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RTN
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RTN
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTN_1.8.0.tar.gz
StartedAt: 2015-10-27 07:38:09 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:40:43 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 154.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RTN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTN_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RTN.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTN’ version ‘1.8.0’
* 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 ‘RTN’ can be installed ... [11s/11s] 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [6s/6s] 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

RTN.Rcheck/00install.out:

* installing *source* package ‘RTN’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (RTN)

RTN.Rcheck/RTN-Ex.timings:

nameusersystemelapsed
AVS-class000
RTN.data0.5040.0160.519
TNA-class0.0010.0000.001
TNI-class0.4920.0090.502
avs.evse000
avs.get0.0000.0000.001
avs.plot10.0000.0000.001
avs.plot20.0000.0000.001
avs.preprocess0.0000.0000.001
avs.vse0.0010.0000.001
tna.get0.5990.0060.605
tna.graph0.3670.0070.373
tna.gsea10.3800.0080.388
tna.gsea20.4040.0070.411
tna.mra0.3690.0050.375
tna.overlap0.3390.0060.344
tna.plot.gsea10.3560.0050.362
tna.plot.gsea20.4100.0060.416
tna.shadow0.3490.0050.353
tna.synergy0.3350.0050.339
tni.bootstrap0.3360.0050.341
tni.conditional0.3930.0060.397
tni.dpi.filter0.4320.0060.439
tni.get0.3550.0070.361
tni.graph0.3450.0040.349
tni.permutation0.3640.0050.370
tni.preprocess1.1190.0441.164
tni2tna.preprocess0.4070.0070.414