Back to "Blame Jeroen" build/check report for BioC 3.11

BUILD BIN report for BiocParallel on tokay2

This page was generated on 2020-04-15 03:20:09 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE BiocParallel PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 17/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.21.2
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: master
Last Commit: 4de8126
Last Changed Date: 2020-04-10 16:25:22 -0400 (Fri, 10 Apr 2020)
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]

Summary

Package: BiocParallel
Version: 1.21.2
Command: rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocParallel.buildbin-libdir BiocParallel_1.21.2.tar.gz
StartedAt: 2020-04-14 23:33:03 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 23:38:04 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 301.7 seconds
RetCode: 0
Status:  OK  
PackageFile: BiocParallel_1.21.2.zip
PackageFileSize: 1.781 MiB

Command output

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### Running command:
###
###   rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocParallel.buildbin-libdir BiocParallel_1.21.2.tar.gz
###
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install for i386

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

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


** libs
/mingw32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/function_types/components.hpp:44,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:11,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/managed_shared_memory.hpp:27,
                 from ipcmutex.cpp:13:
C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/container/string.hpp:405:43: 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/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/container/string.hpp:405:43: 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/bioctesting/bbs-3.11-bioc-testing/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::insert(const char*, const boost::interprocess::ipcdetail::ref_count_ptr&)':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/container/string.hpp:405:43: 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;  }
                                           ^~~~~
/mingw32/bin/g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/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
/mingw64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/function_types/components.hpp:44,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:11,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30,
                 from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/interprocess/managed_shared_memory.hpp:27,
                 from ipcmutex.cpp:13:
C:/Users/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/container/string.hpp:405:43: 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/bioctesting/bbs-3.11-bioc-testing/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/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/container/string.hpp:405:43: 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/bioctesting/bbs-3.11-bioc-testing/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::insert(const char*, const boost::interprocess::ipcdetail::ref_count_ptr&)':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/BH/include/boost/container/string.hpp:405:43: 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;  }
                                           ^~~~~
/mingw64/bin/g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/BiocParallel.buildbin-libdir/BiocParallel/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocParallel' as BiocParallel_1.21.2.zip
* DONE (BiocParallel)