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BioC 3.1: CHECK report for BiocParallel on petty

This page was generated on 2015-10-09 09:35:23 -0700 (Fri, 09 Oct 2015).

Package 95/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.2.22
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BiocParallel
Last Changed Rev: 108966 / Revision: 109384
Last Changed Date: 2015-09-29 12:01:59 -0700 (Tue, 29 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.2.22
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.2.22.tar.gz
StartedAt: 2015-10-08 21:42:07 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 21:46:45 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 278.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.2.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BiocParallel.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.2.22’
* 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 ... [4s/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
.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: 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 ... [51s/60s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
bpvec                7.036  3.792   0.508
bpaggregate          9.036  1.213   9.017
bpmapply             5.503  3.612   1.309
MulticoreParam-class 2.768  1.221   9.487
SnowParam-class      0.315  0.081  20.211
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [98s/171s]
 [98s/172s] 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-3.1-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-class3.1290.0903.672
BiocParallelParam-class0.0030.0000.002
DoparParam-class0.2830.0221.730
MulticoreParam-class2.7681.2219.487
SerialParam-class0.0100.0030.014
SnowParam-class 0.315 0.08120.211
bpaggregate9.0361.2139.017
bpiterate0.0030.0010.005
bplapply0.3890.1322.466
bpmapply5.5033.6121.309
bpok0.1160.0394.547
bpschedule0.0540.0291.182
bpvalidate0.7050.0600.765
bpvec7.0363.7920.508
bpvectorize0.0390.1000.048
register1.6311.1094.012