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CHECK report for BiocParallel on malbec1

This page was generated on 2018-04-12 13:10:47 -0400 (Thu, 12 Apr 2018).

Package 127/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.12.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: RELEASE_3_6
Last Commit: 2143a9a
Last Changed Date: 2017-10-30 12:39:55 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.12.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.12.0.tar.gz
StartedAt: 2018-04-11 21:48:26 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:50:51 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 144.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BiocParallel.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 ... 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
--------------------------------------------------------------------------
[[32041,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec1

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
Unexported objects imported by ':::' calls:
  ‘BatchJobs:::checkDir’ ‘parallel:::closeNode’ ‘parallel:::recvData’
  ‘parallel:::recvOneData’ ‘parallel:::sendData’
  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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘BiocParallel/libs/BiocParallel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ipcmutex.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bpaggregate     5.672  0.232   6.134
SnowParam-class 0.452  0.040   5.026
ipcmutex        0.012  0.084   5.202
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.



Installation output

BiocParallel.Rcheck/00install.out

* installing *source* package ‘BiocParallel’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c ipcmutex.cpp -o ipcmutex.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/config/no_tr1/memory.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/BiocParallel.Rcheck/BiocParallel/libs
** 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)

Tests output

BiocParallel.Rcheck/tests/test.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("BiocParallel")
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Timing stopped at: 0.004 0 0
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
2: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
3: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
4: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
5: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
6: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
7: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
8: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
9: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
10: In result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
--------------------------------------------------------------------------
[[11525,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec1

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
Timing stopped at: 0.08 0.024 0.216
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
test_bpiterate_Params
  chunks greater than number of workers
    ith param
    ith param
    ith param
  chunks less than number of workers [1]
    ith param
    ith param
    ith param
  chunks less than number of workers [2]
    ith param
    ith param
  cleanup
test_bpiterate_Params DONE
test_bpiterate_REDUCE
  setup
    ith param
      no REDUCE
      REDUCE
      'reduce.in.order' FALSE [1]
      'reduce.in.order' FALSE [2]
      'reduce.in.order' TRUE [1]
      'reduce.in.order' TRUE [2]
    ith param
      no REDUCE
      REDUCE
      'reduce.in.order' FALSE [1]
      'reduce.in.order' FALSE [2]
      'reduce.in.order' TRUE [1]
      'reduce.in.order' TRUE [2]
  cleanup
test_bpiterate_REDUCE DONE
test_bplapply_Params
  setup
  sqrt
    serial
    snow
    dopar
    batchjobs
    mc
  empty input
    serial
    snow
    dopar
    batchjobs
    mc
  BatchJobs
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
  cleanup
test_bplapply_Params DONE
test_bplapply_symbols
  setup
    serial
    snow
    dopar
    mc
  cleanup
test_bplapply_symbols DONE
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
resuming previous calculation ... 
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
resuming previous calculation ... 
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
resuming previous calculation ... 
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
resuming previous calculation ... 
resuming previous calculation ... 
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
resuming previous calculation ... 
resuming previous calculation ... 
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
Warning in result_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries


RUNIT TEST PROTOCOL -- Wed Apr 11 21:50:48 2018 
*********************************************** 
Number of test functions: 41 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 29.912   2.376  86.718 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class2.8880.0282.937
BiocParallelParam-class0.0040.0000.001
DoparParam-class0.0000.0000.001
MulticoreParam-class0.4440.1242.628
SerialParam-class0.0120.0040.016
SnowParam-class0.4520.0405.026
bpaggregate5.6720.2326.134
bpiterate0.0040.0000.003
bplapply0.0240.0200.088
bploop000
bpmapply0.0200.0840.158
bpok0.0600.1082.369
bpschedule0.0400.0480.144
bptry0.0440.0760.244
bpvalidate0.2320.0200.255
bpvec0.4520.0640.564
bpvectorize0.0240.0320.109
ipcmutex0.0120.0845.202
register0.0480.0480.189