| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 168/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocParallel 1.26.2 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BiocParallel |
| Version: 1.26.2 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiocParallel_1.26.2.tar.gz |
| StartedAt: 2021-10-14 09:01:47 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:06:55 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 308.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocParallel.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BiocParallel_1.26.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BiocParallel.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.26.2’
* 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 2.258 0.718 10.754
SnowParam-class 0.964 0.019 5.665
* 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-3.13-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.
BiocParallel.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BiocParallel
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* installing to library ‘/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/fold_impl.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/fold.hpp:20,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/remove_if.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/remove.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function_types/components.hpp:44,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function_types/is_member_function_pointer.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tti/detail/dmem_fun.hpp:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/tti/has_member_function.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/uuid/random_generator.hpp:20,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/uuid/uuid_generators.hpp:17,
from ipcmutex.cpp:3:
/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)
BiocParallel.Rcheck/tests/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 0.001 0
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
Timing stopped at: 0.046 0.02 0.531
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> >
RUNIT TEST PROTOCOL -- Thu Oct 14 09:06:52 2021
***********************************************
Number of test functions: 76
Number of deactivated test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocParallel RUnit Tests - 76 test functions, 0 errors, 0 failures
Number of test functions: 76
Number of deactivated test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
78.469 6.528 250.901
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchJobsParam-class | 4.509 | 0.075 | 4.588 | |
| BatchtoolsParam-class | 2.258 | 0.718 | 10.754 | |
| BiocParallelParam-class | 0.000 | 0.002 | 0.003 | |
| DeveloperInterface | 0.000 | 0.001 | 0.000 | |
| DoparParam-class | 0.001 | 0.000 | 0.000 | |
| MulticoreParam-class | 0.914 | 0.336 | 2.662 | |
| SerialParam-class | 0.057 | 0.013 | 0.034 | |
| SnowParam-class | 0.964 | 0.019 | 5.665 | |
| bpaggregate | 0.000 | 0.001 | 0.000 | |
| bpiterate | 0.000 | 0.001 | 0.001 | |
| bplapply | 0.348 | 0.068 | 0.337 | |
| bploop | 0.000 | 0.000 | 0.001 | |
| bpmapply | 0.327 | 0.075 | 0.344 | |
| bpok | 0.396 | 0.008 | 2.083 | |
| bpschedule | 0.263 | 0.034 | 0.286 | |
| bptry | 0.053 | 0.078 | 0.060 | |
| bpvalidate | 3.607 | 0.163 | 3.730 | |
| bpvec | 0.546 | 0.109 | 0.541 | |
| bpvectorize | 0.042 | 0.061 | 0.053 | |
| ipcmutex | 0.481 | 0.154 | 0.929 | |
| register | 0.156 | 0.186 | 0.138 | |