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CHECK report for BiocParallel on malbec2

This page was generated on 2019-10-16 12:02:02 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocParallel_1.18.1.tar.gz
StartedAt: 2019-10-16 00:05:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:11:50 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 363.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocParallel_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocParallel.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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
--------------------------------------------------------------------------
[[38602,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec2

Another transport will be used instead, although this may result in
lower performance.

NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
BatchtoolsParam-class 11.069  0.635  12.987
bpaggregate           10.923  0.575  11.576
bpok                   2.618  0.495  11.471
ipcmutex               1.455  0.473   6.594
SnowParam-class        0.792  0.134   6.292
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.



Installation output

BiocParallel.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ipcmutex.cpp -o ipcmutex.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:17,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use  instead.
 BOOST_HEADER_DEPRECATED("");
                                                           ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 0.001
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
In addition: There were 50 or more warnings (use warnings() to see the first 50)
--------------------------------------------------------------------------
[[46950,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec2

Another transport will be used instead, although this may result in
lower performance.

NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
Timing stopped at: 0.032 0.016 0.32
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> > 

RUNIT TEST PROTOCOL -- Wed Oct 16 00:11:45 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 
158.940   7.769 260.676 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class3.8540.0423.924
BatchtoolsParam-class11.069 0.63512.987
BiocParallelParam-class0.0020.0000.002
DeveloperInterface000
DoparParam-class000
MulticoreParam-class1.2010.2693.160
SerialParam-class0.0360.0370.017
SnowParam-class0.7920.1346.292
bpaggregate10.923 0.57511.576
bpiterate0.0010.0000.001
bplapply0.7640.2420.859
bploop000
bpmapply1.9320.3832.094
bpok 2.618 0.49511.471
bpschedule1.9490.2912.268
bptry1.2840.3271.413
bpvalidate0.2680.0790.237
bpvec1.2620.1371.416
bpvectorize0.6740.2860.779
ipcmutex1.4550.4736.594
register1.4300.5311.668