Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-12-01 17:17:20 -0500 (Wed, 01 Dec 2021).

CHECK results for BiocParallel on nebbiolo2

To the developers/maintainers of the BiocParallel package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 165/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocParallel 1.28.2  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/BiocParallel
git_branch: RELEASE_3_14
git_last_commit: 56dc83d
git_last_commit_date: 2021-11-24 12:26:00 -0500 (Wed, 24 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BiocParallel
Version: 1.28.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiocParallel_1.28.2.tar.gz
StartedAt: 2021-11-30 08:16:02 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 08:21:24 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 322.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocParallel.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiocParallel_1.28.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BiocParallel.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.28.2’
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
BatchtoolsParam-class 2.255  0.701  10.656
SnowParam-class       0.984  0.027   5.423
* 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-3.14-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.



Installation output

BiocParallel.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.14-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>::************
      |                     ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 0 0.001
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
Timing stopped at: 0.027 0.024 0.472
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> > 

RUNIT TEST PROTOCOL -- Tue Nov 30 08:21:20 2021 
*********************************************** 
Number of test functions: 94 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocParallel RUnit Tests - 94 test functions, 0 errors, 0 failures
Number of test functions: 94 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 78.053   7.707 264.661 

Example timings

BiocParallel.Rcheck/BiocParallel-Ex.timings

nameusersystemelapsed
BatchJobsParam-class4.1780.0274.207
BatchtoolsParam-class 2.255 0.70110.656
BiocParallelParam-class0.0020.0000.001
DeveloperInterface000
DoparParam-class0.0010.0000.000
MulticoreParam-class0.9670.3962.699
SerialParam-class0.0610.0300.044
SnowParam-class0.9840.0275.423
bpaggregate000
bpiterate0.0000.0000.001
bplapply0.3700.0730.400
bploop000
bpmapply0.2640.0760.286
bpok0.3730.0032.467
bpschedule0.2560.0130.297
bptry0.0710.0780.066
bpvalidate3.0580.1273.163
bpvec0.4550.1150.458
bpvectorize0.0430.0600.062
ipcmutex0.4310.1650.899
register0.1610.1490.134