##############################################################################
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###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocParallel.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocParallel_1.29.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BiocParallel.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.17'
* 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
* 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.workerLapply_impl'
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
BatchJobsParam-class  3.19   0.14    5.31
BatchtoolsParam-class 0.64   0.11   17.95
SnowParam-class       0.72   0.00    5.72
bpoptions             0.00   0.00    5.16
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.

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##############################################################################
###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BiocParallel' ...
** using staged installation

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


** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ipcmutex.cpp -o ipcmutex.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-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 D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/interprocess/detail/windows_intermodule_singleton.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/interprocess/detail/shared_dir_helpers.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/interprocess/shared_memory_object.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/interprocess/managed_shared_memory.hpp:27,
                 from ipcmutex.cpp:13:
D:/biocbuild/bbs-3.15-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*)':
D:/biocbuild/bbs-3.15-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;  }
                                           ^~~~~
D:/biocbuild/bbs-3.15-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*)':
D:/biocbuild/bbs-3.15-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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BiocParallel/00new/BiocParallel/libs/x64
** 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  
    bpoptions                               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
* DONE (BiocParallel)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'parody' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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: 0.02 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 -- Thu Mar 17 18:39:00 2022 
*********************************************** 
Number of test functions: 97 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 97 test functions, 0 errors, 0 failures
Number of test functions: 97 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  32.15    1.54  282.65 
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