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CHECK report for BiocParallel on celaya2

This page was generated on 2019-10-16 12:50:50 -0400 (Wed, 16 Oct 2019).

Package 150/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.18.1
Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: RELEASE_3_9
Last Commit: 348264a
Last Changed Date: 2019-08-06 13:19:20 -0400 (Tue, 06 Aug 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.18.1
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_1.18.1.tar.gz
StartedAt: 2019-10-16 00:55:13 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:02:37 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 444.4 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

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### Running 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_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BiocParallel.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.1’
* 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           14.134  1.169  15.037
BatchtoolsParam-class  6.212  3.324  12.398
BatchJobsParam-class   4.814  0.225   5.046
ipcmutex               2.110  1.395   8.007
bpok                   2.820  0.093  15.557
SnowParam-class        0.996  0.134   8.834
* 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.



Installation output

BiocParallel.Rcheck/00install.out

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###
### Running command:
###
###   /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’ ...
** using staged installation
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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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  instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("");
^
/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)))
                                 ^
:177:2: note: expanded from here
 message("This header is deprecated. Use " "" " 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/00LOCK-BiocParallel/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0.001 0 0
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
In addition: There were 45 warnings (use warnings() to see them)
Timing stopped at: 0.291 0.04 0.386
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> > 

RUNIT TEST PROTOCOL -- Wed Oct 16 01:02:26 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 
125.972  49.583 304.284 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class4.8140.2255.046
BatchtoolsParam-class 6.212 3.32412.398
BiocParallelParam-class0.0040.0010.005
DeveloperInterface0.0010.0000.000
DoparParam-class0.0000.0000.001
MulticoreParam-class1.7110.9153.623
SerialParam-class0.1090.1490.057
SnowParam-class0.9960.1348.834
bpaggregate14.134 1.16915.037
bpiterate0.0010.0010.003
bplapply0.9410.4581.461
bploop0.0000.0000.001
bpmapply2.4130.9383.202
bpok 2.820 0.09315.557
bpschedule1.9500.0722.073
bptry2.0151.1912.812
bpvalidate0.5480.2930.517
bpvec1.8700.7112.214
bpvectorize0.9440.4941.523
ipcmutex2.1101.3958.007
register2.0961.3822.864