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BioC 3.5: CHECK report for IPO on toluca2

This page was generated on 2017-04-23 14:41:59 -0400 (Sun, 23 Apr 2017).

Package 681/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IPO 1.1.2
Thomas Riebenbauer
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IPO
Last Changed Rev: 128303 / Revision: 129046
Last Changed Date: 2017-04-07 13:22:14 -0400 (Fri, 07 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IPO
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IPO_1.1.2.tar.gz
StartedAt: 2017-04-23 05:37:30 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 05:46:59 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 569.3 seconds
RetCode: 0
Status:  OK 
CheckDir: IPO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IPO_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IPO.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IPO’ version ‘1.1.2’
* 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 ‘IPO’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/IPO.Rcheck/00check.log’
for details.


IPO.Rcheck/00install.out:

* installing *source* package ‘IPO’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IPO)

IPO.Rcheck/IPO-Ex.timings:

nameusersystemelapsed
IPO-package0.0010.0000.001
attachList0.0010.0010.001
calcPPS2.4340.0842.534
calculateXcmsSet3.0930.0633.175
combineParams0.0790.0010.092
createModel0.5580.0050.564
decode0.0030.0010.003
findIsotopes.CAMERA1.8110.0311.927
findIsotopes.IPO2.6650.0472.727
getBbdParameter0.0060.0000.005
getCcdParameter0.0100.0010.010
getDefaultRetCorCenterSample0.0010.0000.002
getDefaultRetGroupStartingParams0.0010.0000.002
getDefaultXcmsSetStartingParams0.0020.0010.002
getNormalizedResponse0.0010.0000.001
getRGTVValues0.0000.0000.001
optimizeRetGroup0.0000.0000.001
optimizeXcmsSet0.0010.0000.001
toMatrix0.0020.0000.002
typeCastParams0.0010.0000.001
writeParamsTable0.0720.0010.073
writeRScript0.0040.0010.004