Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: CHECK report for BiocParallel on moscato2

This page was generated on 2015-10-09 09:30:03 -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: rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.2.22.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.2.22.tar.gz
StartedAt: 2015-10-08 23:42:48 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:48:27 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 339.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.2.22.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.2.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/BiocParallel.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'BiocParallel' can be installed ... 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
* 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BatchJobs:::checkDir' 'parallel:::.check_ncores'
  'parallel:::addClusterOptions' 'parallel:::checkCluster'
  'parallel:::getClusterOption' 'parallel:::recvData'
  'parallel:::recvOneData' 'parallel:::sendCall' 'parallel:::sendData'
  '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
.bpnewForkNode: no visible global function definition for 'mcfork'
.bpnewForkNode: no visible global function definition for 'mcexit'
.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [55s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
bpaggregate          4.52   0.05   12.79
SnowParam-class      0.27   0.03   13.15
bplapply             0.23   0.03    5.25
MulticoreParam-class 0.12   0.00    6.30
** running examples for arch 'x64' ... [61s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
bpaggregate          4.90   0.03   13.92
bplapply             0.36   0.06    6.81
bpvec                0.25   0.04    5.63
SnowParam-class      0.23   0.05   14.26
MulticoreParam-class 0.12   0.00    6.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [86s]
 [86s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [96s]
 [96s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.


BiocParallel.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'BiocParallel' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocParallel' as BiocParallel_1.2.22.zip
* DONE (BiocParallel)

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

nameusersystemelapsed
BatchJobsParam-class2.140.153.18
BiocParallelParam-class000
DoparParam-class0.090.030.76
MulticoreParam-class0.120.006.30
SerialParam-class0.020.000.02
SnowParam-class 0.27 0.0313.15
bpaggregate 4.52 0.0512.79
bpiterate000
bplapply0.230.035.25
bpmapply0.020.000.01
bpok0.050.032.25
bpschedule0.010.000.01
bpvalidate0.330.000.33
bpvec0.190.024.78
bpvectorize0.020.064.37
register0.050.031.17

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

nameusersystemelapsed
BatchJobsParam-class2.080.062.36
BiocParallelParam-class000
DoparParam-class0.130.030.94
MulticoreParam-class0.120.006.30
SerialParam-class000
SnowParam-class 0.23 0.0514.26
bpaggregate 4.90 0.0313.92
bpiterate000
bplapply0.360.066.81
bpmapply0.020.000.01
bpok0.070.043.89
bpschedule0.020.000.01
bpvalidate0.270.030.30
bpvec0.250.045.63
bpvectorize0.040.024.66
register0.070.031.70