##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocParallel.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocParallel_1.30.4.tar.gz
###
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##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/BiocParallel.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.30.4'
* 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 'F:/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)

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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
BatchJobsParam-class  5.06   0.30    5.47
ipcmutex              1.27   0.05    5.66
SnowParam-class       1.16   0.02    6.70
BatchtoolsParam-class 0.64   0.13   18.25
bpvectorize           0.45   0.00    5.39
bpoptions             0.00   0.00    5.15
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocParallel
###
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* installing to library 'F:/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
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ipcmutex.cpp -o ipcmutex.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
F:/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]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def ipcmutex.o -lbcrypt -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/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
** 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)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
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 0 0
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
setting timeout 1
setting timeout 1


RUNIT TEST PROTOCOL -- Tue Oct 18 22:29:38 2022 
*********************************************** 
Number of test functions: 102 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 102 test functions, 0 errors, 0 failures
Number of test functions: 102 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  48.18    2.23  364.21 
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