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BioC 3.0: CHECK report for RPA on moscato1

This page was generated on 2015-04-10 09:45:52 -0700 (Fri, 10 Apr 2015).

Package 770/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RPA 1.22.0
Leo Lahti
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/RPA
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: RPA
Version: 1.22.0
Command: rm -rf RPA.buildbin-libdir RPA.Rcheck && mkdir RPA.buildbin-libdir RPA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RPA.buildbin-libdir RPA_1.22.0.tar.gz >RPA.Rcheck\00install.out 2>&1 && cp RPA.Rcheck\00install.out RPA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RPA.buildbin-libdir --install="check:RPA-install.out" --force-multiarch --no-vignettes --timings RPA_1.22.0.tar.gz
StartedAt: 2015-04-10 05:12:32 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:14:21 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 109.1 seconds
RetCode: 0
Status:  OK  
CheckDir: RPA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RPA.buildbin-libdir RPA.Rcheck && mkdir RPA.buildbin-libdir RPA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RPA.buildbin-libdir RPA_1.22.0.tar.gz >RPA.Rcheck\00install.out 2>&1 && cp RPA.Rcheck\00install.out RPA-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RPA.buildbin-libdir --install="check:RPA-install.out" --force-multiarch --no-vignettes --timings RPA_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/RPA.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RPA' version '1.22.0'
* 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 whether package 'RPA' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 ... NOTE
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RPA.preprocess: no visible global function definition for 'normalize'
estimate.hyperparameters: no visible global function definition for
  'mclapply'
get.affinities: no visible global function definition for 'mclapply'
summarize.batch: no visible global function definition for 'mclapply'
updating.hyperparameters: no visible global function definition for
  'mclapply'
* 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' ... [1s] OK
** running examples for arch 'x64' ... [2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'rpa.R' [19s]
 [20s] OK
** running tests for arch 'x64' ...
  Running 'rpa.R' [22s]
 [23s] OK
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/RPA.Rcheck/00check.log'
for details.

RPA.Rcheck/00install.out:


install for i386

* installing *source* package 'RPA' ...
** 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 'RPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RPA' as RPA_1.22.0.zip
* DONE (RPA)

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

nameusersystemelapsed
RPA-package000
RPA.iteration000
RPA.preprocess000
collect.hyperparameters000
d.update.fast000
estimate.affinities000
estimate.hyperparameters000
frpa000
get.batches000
get.probe.matrix000
get.probe.parameters000
hyperparameter.update000
online.quantile000
probe.parameters.tolist000
probe.performance000
probeplot000
probetable000
rpa000
rpa.complete000
rpa.fit000
rpa.online000
rpa.plot000
rpa.summarize000
rpaplot000
sample.probeset000
summarize.batch000
summarize.batches000
updating.hyperparameters000

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

nameusersystemelapsed
RPA-package000
RPA.iteration000
RPA.preprocess000
collect.hyperparameters000
d.update.fast000
estimate.affinities000
estimate.hyperparameters000
frpa000
get.batches000
get.probe.matrix000
get.probe.parameters000
hyperparameter.update000
online.quantile000
probe.parameters.tolist000
probe.performance000
probeplot000
probetable000
rpa000
rpa.complete000
rpa.fit000
rpa.online000
rpa.plot000
rpa.summarize0.010.000.01
rpaplot000
sample.probeset000
summarize.batch000
summarize.batches000
updating.hyperparameters000