| Back to Multiple platform build/check report for BioC 3.11 (small subset of software packages ONLY) |
This page was generated on 2020-01-24 03:57:02 -0500 (Fri, 24 Jan 2020).
| Package 10/41 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| BiocParallel 1.21.2 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | [ OK ] | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped |
| Package: BiocParallel |
| Version: 1.21.2 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BiocParallel_1.21.2.tar.gz |
| StartedAt: 2020-01-24 03:04:18 -0500 (Fri, 24 Jan 2020) |
| EndedAt: 2020-01-24 03:10:44 -0500 (Fri, 24 Jan 2020) |
| EllapsedTime: 386.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocParallel.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BiocParallel_1.21.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/BiocParallel.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* 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 ‘1.21.2’
* 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
--------------------------------------------------------------------------
[[60024,1],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 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 11.289 0.612 14.211
SnowParam-class 0.921 0.203 6.672
* 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-3.11-bioc-testing/meat/BiocParallel.Rcheck/00check.log’
for details.
BiocParallel.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BiocParallel ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’ * 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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc-testing/Rlibs/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 Under development (unstable) (2019-12-14 r77569) -- "Unsuffered Consequences"
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 0 0
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
--------------------------------------------------------------------------
[[51398,1],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: 0.022 0.024 0.337
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> >
RUNIT TEST PROTOCOL -- Fri Jan 24 03:10:39 2020
***********************************************
Number of test functions: 75
Number of deactivated test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocParallel RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75
Number of deactivated test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
189.581 10.338 308.632
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchJobsParam-class | 4.593 | 0.072 | 4.818 | |
| BatchtoolsParam-class | 11.289 | 0.612 | 14.211 | |
| BiocParallelParam-class | 0.002 | 0.000 | 0.002 | |
| DeveloperInterface | 0 | 0 | 0 | |
| DoparParam-class | 0.000 | 0.000 | 0.001 | |
| MulticoreParam-class | 0.922 | 0.465 | 2.805 | |
| SerialParam-class | 0.024 | 0.005 | 0.019 | |
| SnowParam-class | 0.921 | 0.203 | 6.672 | |
| bpaggregate | 0.002 | 0.000 | 0.003 | |
| bpiterate | 0.001 | 0.000 | 0.001 | |
| bplapply | 0.331 | 0.139 | 0.457 | |
| bploop | 0 | 0 | 0 | |
| bpmapply | 0.273 | 0.099 | 0.344 | |
| bpok | 0.414 | 0.111 | 3.009 | |
| bpschedule | 0.304 | 0.058 | 0.358 | |
| bptry | 0.038 | 0.076 | 0.071 | |
| bpvalidate | 4.189 | 0.092 | 4.257 | |
| bpvec | 0.533 | 0.092 | 0.586 | |
| bpvectorize | 0.004 | 0.081 | 0.068 | |
| ipcmutex | 0.449 | 0.228 | 0.963 | |
| register | 0.082 | 0.207 | 0.162 | |