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CHECK report for BiocParallel on merida1

This page was generated on 2020-04-15 12:38:18 -0400 (Wed, 15 Apr 2020).

Package 156/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.20.1
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BiocParallel
Branch: RELEASE_3_10
Last Commit: 374b87c
Last Changed Date: 2019-12-20 17:35:14 -0400 (Fri, 20 Dec 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocParallel
Version: 1.20.1
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_1.20.1.tar.gz
StartedAt: 2020-04-15 00:41:59 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:47:35 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 335.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiocParallel.Rcheck
Warnings: 1

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_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BiocParallel.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.1’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'bpschedule':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
BatchtoolsParam-class 6.233  2.647  11.710
bpvalidate            4.911  0.242   5.231
SnowParam-class       0.800  0.059   6.973
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-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
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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
Timing stopped at: 0.195 0.022 0.259
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> > 

RUNIT TEST PROTOCOL -- Wed Apr 15 00:47:26 2020 
*********************************************** 
Number of test functions: 74 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
109.799  64.629 254.885 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class4.0260.1114.344
BatchtoolsParam-class 6.233 2.64711.710
BiocParallelParam-class0.0030.0010.003
DeveloperInterface0.0000.0000.001
DoparParam-class0.0010.0000.001
MulticoreParam-class1.0240.5682.810
SerialParam-class0.0200.0030.026
SnowParam-class0.8000.0596.973
bpaggregate0.0020.0000.002
bpiterate0.0010.0010.002
bplapply0.2910.0660.312
bploop0.0010.0000.000
bpmapply0.2800.0970.373
bpok0.3290.0183.255
bpschedule0.2080.0460.240
bptry0.0700.0820.096
bpvalidate4.9110.2425.231
bpvec0.4260.0620.449
bpvectorize0.0360.0560.046
ipcmutex0.4320.1750.978
register0.0910.1090.128