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This page was generated on 2024-05-22 11:36:37 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4665
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4400
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4427
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

Package 185/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.39.0  (landing page)
Martin Morgan
Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/BiocParallel
git_branch: devel
git_last_commit: aa329b3
git_last_commit_date: 2024-04-30 10:29:39 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for BiocParallel on palomino4


To the developers/maintainers of the BiocParallel package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BiocParallel
Version: 1.39.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocParallel.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocParallel_1.39.0.tar.gz
StartedAt: 2024-05-20 22:35:51 -0400 (Mon, 20 May 2024)
EndedAt: 2024-05-20 22:44:08 -0400 (Mon, 20 May 2024)
EllapsedTime: 497.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocParallel.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocParallel_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BiocParallel.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocParallel/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocParallel' version '1.39.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 code 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
':::' calls which should be '::':
  '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-3.20-bioc/R/library/BiocParallel/libs/x64/BiocParallel.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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
BatchtoolsParam-class 1.44   0.14   25.78
ipcmutex              1.11   0.06    5.53
SnowParam-class       1.13   0.01    6.59
bptry                 0.21   0.03    5.13
bpoptions             0.01   0.00    5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.


Installation output

BiocParallel.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BiocParallel' ...
** using staged installation

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


** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/cpp11/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp11.cpp -o cpp11.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/cpp11/include'   -I"C:/rtools44/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-3.20-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-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>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++ -shared -s -static-libgcc -o BiocParallel.dll tmp.def cpp11.o ipcmutex.o -lbcrypt -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-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)

Tests output

BiocParallel.Rcheck/tests/test.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
Testing BatchtoolsParam
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' ...
> > > > > > > > > > > > > > > > > > > > > > > > > > > Testing BiocParallelParam
Testing DoparParam
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
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
Testing MulticoreParam
Testing SerialParam
Testing SnowParam
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
Testing bpaggregate
Testing bpexportglobals
Testing bpiterate
Testing bplapply
Testing bploop
Testing bpmapply
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
Testing bpoptions
Testing bpvalidate
Testing bpvec
Testing bpvectorize
Testing errorhandling
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
loaded BiocParallel and set parent environment
Testing internal_rng_stream
Testing ipcmutex
Testing logging
Testing refclass
Testing rng
Testing utilities
Testing worker-number


RUNIT TEST PROTOCOL -- Mon May 20 22:43:50 2024 
*********************************************** 
Number of test functions: 109 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 109 test functions, 0 errors, 0 failures
Number of test functions: 109 
Number of deactivated test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  42.35    2.68  336.96 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchtoolsParam-class 1.44 0.1425.78
BiocParallelParam-class0.000.000.01
DeveloperInterface000
DoparParam-class000
MulticoreParam-class0.620.022.66
SerialParam-class0.030.000.03
SnowParam-class1.130.016.59
bpaggregate000
bpiterate0.340.021.97
bplapply0.130.052.43
bploop000
bpmapply0.280.001.17
bpok0.470.063.41
bpoptions0.010.005.11
bpschedule0.460.000.45
bptry0.210.035.13
bpvalidate3.710.273.96
bpvec0.840.032.86
bpvectorize0.410.053.68
ipcmutex1.110.065.53
register1.000.033.16
worker-number1.390.001.39