| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:02:02 -0400 (Wed, 16 Oct 2019).
| Package 150/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocParallel 1.18.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### /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
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* 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.
BiocParallel.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocParallel
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* 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)
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
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchJobsParam-class | 3.854 | 0.042 | 3.924 | |
| BatchtoolsParam-class | 11.069 | 0.635 | 12.987 | |
| BiocParallelParam-class | 0.002 | 0.000 | 0.002 | |
| DeveloperInterface | 0 | 0 | 0 | |
| DoparParam-class | 0 | 0 | 0 | |
| MulticoreParam-class | 1.201 | 0.269 | 3.160 | |
| SerialParam-class | 0.036 | 0.037 | 0.017 | |
| SnowParam-class | 0.792 | 0.134 | 6.292 | |
| bpaggregate | 10.923 | 0.575 | 11.576 | |
| bpiterate | 0.001 | 0.000 | 0.001 | |
| bplapply | 0.764 | 0.242 | 0.859 | |
| bploop | 0 | 0 | 0 | |
| bpmapply | 1.932 | 0.383 | 2.094 | |
| bpok | 2.618 | 0.495 | 11.471 | |
| bpschedule | 1.949 | 0.291 | 2.268 | |
| bptry | 1.284 | 0.327 | 1.413 | |
| bpvalidate | 0.268 | 0.079 | 0.237 | |
| bpvec | 1.262 | 0.137 | 1.416 | |
| bpvectorize | 0.674 | 0.286 | 0.779 | |
| ipcmutex | 1.455 | 0.473 | 6.594 | |
| register | 1.430 | 0.531 | 1.668 | |