Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:05:57 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

INSTALL 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? here 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: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 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 -0500 (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:\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
StartedAt: 2022-01-16 04:24:44 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 04:30:48 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 364.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  132k  100  132k    0     0   984k      0 --:--:-- --:--:-- --:--:--  993k

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