Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BiocParallel |
| Branch: master |
| Last Commit: 3bc700d |
| Last Changed Date: 2019-03-23 18:00:55 -0400 (Sat, 23 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:27:44 -0400 (Tue, 09 Apr 2019).
| Package 147/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocParallel 1.17.18 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: BiocParallel |
| Version: 1.17.18 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocParallel_1.17.18.tar.gz |
| StartedAt: 2019-04-08 23:29:56 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:35:15 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 319.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocParallel.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocParallel_1.17.18.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocParallel.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.17.18’
* 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 for sufficient/correct file permissions ... 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.
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpaggregate 9.123 1.083 10.129
BatchtoolsParam-class 5.316 2.970 11.306
ipcmutex 0.235 0.267 5.266
SnowParam-class 0.396 0.066 6.414
bpok 0.164 0.076 9.715
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.
BiocParallel.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocParallel
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BiocParallel’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ipcmutex.cpp -o ipcmutex.o
In file included from ipcmutex.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/uuid/uuid_generators.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/uuid/random_generator.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/mersenne_twister.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/seed_impl.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
^
<scratch space>:157:2: note: expanded from here
message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiocParallel/libs
** 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
* DONE (BiocParallel)
BiocParallel.Rcheck/tests/test.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 'Multicore' ...
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 'Multicore' ...
> > > > > > > > > > > > > > > > Timing stopped at: 0 0 0.001
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
In addition: There were 43 warnings (use warnings() to see them)
Timing stopped at: 0.184 0.023 0.246
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> >
RUNIT TEST PROTOCOL -- Mon Apr 8 23:35:07 2019
***********************************************
Number of test functions: 69
Number of deactivated test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocParallel RUnit Tests - 69 test functions, 0 errors, 0 failures
Number of test functions: 69
Number of deactivated test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
87.709 64.911 228.537
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchJobsParam-class | 3.410 | 0.101 | 3.599 | |
| BatchtoolsParam-class | 5.316 | 2.970 | 11.306 | |
| BiocParallelParam-class | 0.001 | 0.001 | 0.002 | |
| DeveloperInterface | 0 | 0 | 0 | |
| DoparParam-class | 0.001 | 0.000 | 0.000 | |
| MulticoreParam-class | 0.758 | 0.411 | 2.555 | |
| SerialParam-class | 0.062 | 0.064 | 0.033 | |
| SnowParam-class | 0.396 | 0.066 | 6.414 | |
| bpaggregate | 9.123 | 1.083 | 10.129 | |
| bpiterate | 0.001 | 0.002 | 0.003 | |
| bplapply | 0.071 | 0.074 | 0.201 | |
| bploop | 0 | 0 | 0 | |
| bpmapply | 0.138 | 0.169 | 0.145 | |
| bpok | 0.164 | 0.076 | 9.715 | |
| bpschedule | 0.059 | 0.048 | 0.143 | |
| bptry | 0.251 | 0.320 | 0.300 | |
| bpvalidate | 0.370 | 0.236 | 0.347 | |
| bpvec | 0.817 | 0.343 | 0.956 | |
| bpvectorize | 0.057 | 0.050 | 0.154 | |
| ipcmutex | 0.235 | 0.267 | 5.266 | |
| register | 0.302 | 0.332 | 0.316 | |