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BioC 3.2: CHECK report for BiocParallel on perceval

This page was generated on 2015-10-27 17:35:19 -0400 (Tue, 27 Oct 2015).

Package 100/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.4.0
Bioconductor Package Maintainer
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/BiocParallel
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  OK  OK  TIMEOUT 
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.4.0.tar.gz
StartedAt: 2015-10-27 05:49:07 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:52:36 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 208.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiocParallel.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocParallel’ version ‘1.4.0’
* 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 ‘BiocParallel’ can be installed ... [3s/4s] 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BatchJobs:::checkDir’ ‘parallel:::.check_ncores’
  ‘parallel:::addClusterOptions’ ‘parallel:::checkCluster’
  ‘parallel:::children’ ‘parallel:::closeStdout’
  ‘parallel:::getClusterOption’ ‘parallel:::isChild’
  ‘parallel:::mc.advance.stream’ ‘parallel:::mc.set.stream’
  ‘parallel:::mcexit’ ‘parallel:::mcfork’ ‘parallel:::mckill’
  ‘parallel:::processID’ ‘parallel:::readChild’ ‘parallel:::recvData’
  ‘parallel:::recvOneData’ ‘parallel:::selectChildren’
  ‘parallel:::sendCall’ ‘parallel:::sendData’ ‘parallel:::sendMaster’
  ‘parallel:::sinkWorkerOutput’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.clear_cluster : <anonymous>: no visible global function definition for
  ‘conditionmessage’
.initiateLogging: no visible global function definition for
  ‘clusterExport’
.initiateLogging : .bufferload : fun: no visible binding for '<<-'
  assignment to ‘buffer’
.initiateLogging : .bufferload : fun: no visible binding for global
  variable ‘buffer’
.try : handler_error: no visible binding for '<<-' assignment to
  ‘success’
.try_log : handler_error: no visible binding for '<<-' assignment to
  ‘success’
bprunMPIslave: no visible global function definition for
  ‘mpi.comm.get.parent’
bprunMPIslave: no visible global function definition for
  ‘mpi.intercomm.merge’
bprunMPIslave: no visible global function definition for
  ‘mpi.comm.set.errhandler’
bprunMPIslave: no visible global function definition for
  ‘mpi.comm.disconnect’
bprunMPIslave: no visible global function definition for
  ‘makeMPImaster’
bprunMPIslave: no visible global function definition for ‘mpi.quit’
bpslaveLoop: no visible binding for '<<-' assignment to ‘buffer’
bpslaveLoop: no visible binding for '<<-' assignment to ‘success’
bpslaveLoop: no visible global function definition for ‘closeNode’
bpslaveLoop : handler: no visible binding for '<<-' assignment to
  ‘success’
bpslaveLoop: no visible binding for global variable ‘success’
bpslaveLoop: no visible binding for global variable ‘buffer’
bpslaveLoop: no visible binding for global variable ‘sout’
bpbackend,BatchJobsParam: no visible global function definition for
  ‘getConfig’
bpisup,DoparParam: no visible global function definition for
  ‘getDoParRegistered’
bpisup,DoparParam: no visible global function definition for
  ‘getDoParName’
bpisup,DoparParam: no visible global function definition for
  ‘getDoParWorkers’
bplapply,ANY-BatchJobsParam: no visible global function definition for
  ‘getConfig’
bplapply,ANY-BatchJobsParam: no visible global function definition for
  ‘setConfig’
bplapply,ANY-BatchJobsParam: no visible global function definition for
  ‘batchMap’
bplapply,ANY-BatchJobsParam: no visible binding for global variable
  ‘submitJobs’
bplapply,ANY-BatchJobsParam: no visible global function definition for
  ‘waitForJobs’
bplapply,ANY-BatchJobsParam: no visible global function definition for
  ‘loadResults’
bplapply,ANY-DoparParam: no visible global function definition for
  ‘%dopar%’
bplapply,ANY-DoparParam: no visible global function definition for
  ‘foreach’
bpstart,SnowParam : .local: no visible global function definition for
  ‘clusterSetRNGStream’
bpstart,SnowParam : .local: no visible global function definition for
  ‘clusterExport’
bpvec,ANY-MulticoreParam: no visible binding for global variable ‘id’
bpworkers,DoparParam: no visible global function definition for
  ‘getDoParWorkers’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/35s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bpvec           7.300  4.143   0.453
bpaggregate     8.970  1.583   8.170
SnowParam-class 0.147  0.044   8.543
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [85s/139s]
 [86s/140s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.


BiocParallel.Rcheck/00install.out:

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

BiocParallel.Rcheck/BiocParallel-Ex.timings:

nameusersystemelapsed
BatchJobsParam-class2.5050.0642.628
BiocParallelParam-class0.0030.0010.003
DoparParam-class0.0010.0010.001
MulticoreParam-class0.8920.3853.737
SerialParam-class0.0070.0020.009
SnowParam-class0.1470.0448.543
bpaggregate8.9701.5838.170
bpiterate0.0030.0010.004
bplapply0.0830.0631.963
bpmapply0.0060.0090.015
bpok0.0930.0343.381
bpschedule0.0440.0211.132
bpvalidate1.9570.9080.691
bpvec7.3004.1430.453
bpvectorize0.0120.0270.024
register2.2791.5273.330