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) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-22 11:36:37 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 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 185/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocParallel 1.39.0 (landing page) Martin Morgan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| 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 |
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###
### 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
###
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* 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.
BiocParallel.Rcheck/00install.out
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###
### 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)
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
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchtoolsParam-class | 1.44 | 0.14 | 25.78 | |
| BiocParallelParam-class | 0.00 | 0.00 | 0.01 | |
| DeveloperInterface | 0 | 0 | 0 | |
| DoparParam-class | 0 | 0 | 0 | |
| MulticoreParam-class | 0.62 | 0.02 | 2.66 | |
| SerialParam-class | 0.03 | 0.00 | 0.03 | |
| SnowParam-class | 1.13 | 0.01 | 6.59 | |
| bpaggregate | 0 | 0 | 0 | |
| bpiterate | 0.34 | 0.02 | 1.97 | |
| bplapply | 0.13 | 0.05 | 2.43 | |
| bploop | 0 | 0 | 0 | |
| bpmapply | 0.28 | 0.00 | 1.17 | |
| bpok | 0.47 | 0.06 | 3.41 | |
| bpoptions | 0.01 | 0.00 | 5.11 | |
| bpschedule | 0.46 | 0.00 | 0.45 | |
| bptry | 0.21 | 0.03 | 5.13 | |
| bpvalidate | 3.71 | 0.27 | 3.96 | |
| bpvec | 0.84 | 0.03 | 2.86 | |
| bpvectorize | 0.41 | 0.05 | 3.68 | |
| ipcmutex | 1.11 | 0.06 | 5.53 | |
| register | 1.00 | 0.03 | 3.16 | |
| worker-number | 1.39 | 0.00 | 1.39 | |