Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:14 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BiocParallel on tokay2


To the developers/maintainers of the BiocParallel package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocParallel.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 165/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.28.3  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/BiocParallel
git_branch: RELEASE_3_14
git_last_commit: 2f9d88a
git_last_commit_date: 2021-12-07 12:12:17 -0400 (Tue, 07 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocParallel
Version: 1.28.3
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocParallel.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocParallel_1.28.3.tar.gz
StartedAt: 2022-04-12 16:17:52 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:32:33 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 881.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocParallel.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocParallel_1.28.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocParallel.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.28.3'
* 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:
  '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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BiocParallel/libs/i386/BiocParallel.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BiocParallel/libs/x64/BiocParallel.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ipcmutex              1.07   0.03    5.64
BatchtoolsParam-class 0.95   0.08   21.51
SnowParam-class       0.94   0.00    7.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ipcmutex              1.32   0.05    7.16
SnowParam-class       1.02   0.00    7.63
BatchtoolsParam-class 0.88   0.09   18.79
bptry                 0.30   0.00    5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.



Installation output

BiocParallel.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BiocParallel_1.28.3.tar.gz && rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocParallel.buildbin-libdir BiocParallel_1.28.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BiocParallel_1.28.3.zip && rm BiocParallel_1.28.3.tar.gz BiocParallel_1.28.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  132k  100  132k    0     0   580k      0 --:--:-- --:--:-- --:--:--  584k

install for i386

* installing *source* package 'BiocParallel' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ipcmutex.cpp -o ipcmutex.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/managed_shared_memory.hpp:27,
                 from ipcmutex.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'bool boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::erase(const char*)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/string.hpp:406:43: warning: '<anonymous>.boost::container::dtl::basic_string_base<boost::container::new_allocator<char> >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    {  return this->members_.plong_repr()->start;  }
                                           ^~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocParallel.buildbin-libdir/00LOCK-BiocParallel/00new/BiocParallel/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocParallel'
    finding HTML links ... done
    BatchJobsParam-class                    html  
    BatchtoolsParam-class                   html  
    BiocParallel-package                    html  
    BiocParallelParam-class                 html  
    DeveloperInterface                      html  
    DoparParam-class                        html  
    MulticoreParam-class                    html  
    SerialParam-class                       html  
    SnowParam-class                         html  
    bpaggregate                             html  
    bpiterate                               html  
    bplapply                                html  
    bploop                                  html  
    bpmapply                                html  
    bpok                                    html  
    bpschedule                              html  
    bptry                                   html  
    bpvalidate                              html  
    bpvec                                   html  
    bpvectorize                             html  
    ipcmutex                                html  
    register                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BiocParallel' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ipcmutex.cpp -o ipcmutex.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/interprocess/managed_shared_memory.hpp:27,
                 from ipcmutex.cpp:13:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'boost::interprocess::ipcdetail::ref_count_ptr* boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::find(const char*)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/string.hpp:406:43: warning: '<anonymous>.boost::container::dtl::basic_string_base<boost::container::new_allocator<char> >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    {  return this->members_.plong_repr()->start;  }
                                           ^~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/string.hpp: In member function 'bool boost::interprocess::ipcdetail::intermodule_singleton_helpers::windows_semaphore_based_map::erase(const char*)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/string.hpp:406:43: warning: '<anonymous>.boost::container::dtl::basic_string_base<boost::container::new_allocator<char> >::long_t::start' may be used uninitialized in this function [-Wmaybe-uninitialized]
    {  return this->members_.plong_repr()->start;  }
                                           ^~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocParallel.buildbin-libdir/BiocParallel/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocParallel' as BiocParallel_1.28.3.zip
* DONE (BiocParallel)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BiocParallel' successfully unpacked and MD5 sums checked

Tests output

BiocParallel.Rcheck/tests_i386/test.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > > > > > > > > > > > > > > > > > > > > > > > > Timing stopped at: 0.02 0 0.02
Error in DEACTIVATED("'DoparParam' orchestration error test not run on Windows") : 
  'DoparParam' orchestration error test not run on Windows
Timing stopped at: 0 0 0
Error in DEACTIVATED("MPI tests not run on Windows") : 
  MPI tests not run on Windows
Timing stopped at: 0 0 0
Error in DEACTIVATED("MPI tests not run on Windows") : 
  MPI tests not run on Windows
> > 

RUNIT TEST PROTOCOL -- Tue Apr 12 16:27:07 2022 
*********************************************** 
Number of test functions: 93 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 93 test functions, 0 errors, 0 failures
Number of test functions: 93 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  38.65    2.09  355.17 
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection

BiocParallel.Rcheck/tests_x64/test.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
> > > > > > > > > > > > > > > > > > > > > > > > > > > Timing stopped at: 0.01 0 0.02
Error in DEACTIVATED("'DoparParam' orchestration error test not run on Windows") : 
  'DoparParam' orchestration error test not run on Windows
Timing stopped at: 0 0 0
Error in DEACTIVATED("MPI tests not run on Windows") : 
  MPI tests not run on Windows
Timing stopped at: 0.01 0 0.02
Error in DEACTIVATED("MPI tests not run on Windows") : 
  MPI tests not run on Windows
> > 

RUNIT TEST PROTOCOL -- Tue Apr 12 16:32:23 2022 
*********************************************** 
Number of test functions: 93 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 93 test functions, 0 errors, 0 failures
Number of test functions: 93 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  42.20    1.73  316.29 
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection

Example timings

BiocParallel.Rcheck/examples_i386/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class4.170.144.86
BatchtoolsParam-class 0.95 0.0821.51
BiocParallelParam-class000
DeveloperInterface000
DoparParam-class0.010.000.01
MulticoreParam-class0.430.002.49
SerialParam-class0.010.000.01
SnowParam-class0.940.007.50
bpaggregate000
bpiterate000
bplapply0.330.032.75
bploop000
bpmapply0.390.021.85
bpok0.390.003.86
bpschedule0.160.000.16
bptry0.250.004.75
bpvalidate3.500.213.71
bpvec0.820.023.27
bpvectorize0.430.023.11
ipcmutex1.070.035.64
register0.500.002.69

BiocParallel.Rcheck/examples_x64/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class4.730.144.95
BatchtoolsParam-class 0.88 0.0918.79
BiocParallelParam-class000
DeveloperInterface000
DoparParam-class000
MulticoreParam-class0.480.022.56
SerialParam-class0.020.000.01
SnowParam-class1.020.007.63
bpaggregate000
bpiterate000
bplapply0.350.002.75
bploop000
bpmapply0.420.011.84
bpok0.460.034.09
bpschedule0.150.000.16
bptry0.300.005.08
bpvalidate3.560.163.72
bpvec0.910.034.75
bpvectorize0.470.033.97
ipcmutex1.320.057.16
register0.540.002.78