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BioC 3.5: CHECK report for IPO on tokay2

This page was generated on 2017-08-16 13:26:04 -0400 (Wed, 16 Aug 2017).

Package 683/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IPO 1.2.1
Thomas Riebenbauer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/IPO
Last Changed Rev: 130969 / Revision: 131943
Last Changed Date: 2017-07-05 13:15:58 -0400 (Wed, 05 Jul 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
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: 1.2.1
Command: rm -rf IPO.buildbin-libdir IPO.Rcheck && mkdir IPO.buildbin-libdir IPO.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IPO.buildbin-libdir IPO_1.2.1.tar.gz >IPO.Rcheck\00install.out 2>&1 && cp IPO.Rcheck\00install.out IPO-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=IPO.buildbin-libdir --install="check:IPO-install.out" --force-multiarch --no-vignettes --timings IPO_1.2.1.tar.gz
StartedAt: 2017-08-16 00:41:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:56:51 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 940.4 seconds
RetCode: 0
Status:  OK  
CheckDir: IPO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IPO.buildbin-libdir IPO.Rcheck && mkdir IPO.buildbin-libdir IPO.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IPO.buildbin-libdir IPO_1.2.1.tar.gz >IPO.Rcheck\00install.out 2>&1 && cp IPO.Rcheck\00install.out IPO-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=IPO.buildbin-libdir --install="check:IPO-install.out" --force-multiarch --no-vignettes --timings IPO_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/IPO.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IPO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IPO' version '1.2.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/IPO.Rcheck/00check.log'
for details.


IPO.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'IPO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IPO' as IPO_1.2.1.zip
* DONE (IPO)

IPO.Rcheck/examples_i386/IPO-Ex.timings:

nameusersystemelapsed
IPO-package000
attachList000
calcPPS2.280.093.36
calculateXcmsSet2.230.072.29
combineParams0.030.000.03
createModel0.370.000.38
decode000
findIsotopes.CAMERA1.350.061.40
findIsotopes.IPO2.120.062.19
getBbdParameter000
getCcdParameter000
getDefaultRetCorCenterSample000
getDefaultRetGroupStartingParams0.000.020.01
getDefaultXcmsSetStartingParams000
getNormalizedResponse000
getRGTVValues000
optimizeRetGroup000
optimizeXcmsSet000
toMatrix000
typeCastParams000
writeParamsTable0.050.000.05
writeRScript000

IPO.Rcheck/examples_x64/IPO-Ex.timings:

nameusersystemelapsed
IPO-package000
attachList000
calcPPS2.890.103.51
calculateXcmsSet3.050.033.08
combineParams0.060.000.06
createModel0.490.000.49
decode000
findIsotopes.CAMERA1.860.031.89
findIsotopes.IPO2.970.033.00
getBbdParameter0.010.000.01
getCcdParameter000
getDefaultRetCorCenterSample000
getDefaultRetGroupStartingParams0.000.020.02
getDefaultXcmsSetStartingParams000
getNormalizedResponse000
getRGTVValues000
optimizeRetGroup000
optimizeXcmsSet000
toMatrix000
typeCastParams000
writeParamsTable0.050.000.05
writeRScript000