| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:38 -0400 (Tue, 16 Apr 2019).
| Package 142/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocParallel 1.16.6 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | ERROR | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: BiocParallel |
| Version: 1.16.6 |
| 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_1.16.6.tar.gz |
| StartedAt: 2019-04-15 22:35:57 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:42:29 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 391.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BiocParallel.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.16.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BiocParallel.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.6’
* 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:
‘BatchJobs:::checkDir’ ‘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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BatchtoolsParam-class 5.265 3.833 11.403
bpaggregate 7.932 0.498 8.373
SnowParam-class 0.398 0.065 5.995
ipcmutex 0.186 0.242 5.254
bpok 0.144 0.068 9.014
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
ERROR
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
test_SnowParam.R
test_SnowParam_MPI
test_SnowParam_coerce_from_MPI
test_bpiterate.R
test_bpiterate_REDUCE
Error in BiocGenerics:::testPackage("BiocParallel") :
unit tests failed for package BiocParallel
Execution halted
Error: failed to stop 'SOCKcluster' cluster: invalid connection
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
* 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 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.
BiocParallel.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocParallel
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BiocParallel’ ...
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/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ipcmutex.cpp -o ipcmutex.o
In file included from ipcmutex.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/uuid/uuid_generators.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/uuid/random_generator.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/mersenne_twister.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/seed_impl.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
^
<scratch space>:157:2: note: expanded from here
message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
^
1 warning generated.
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/3.5/Resources/library/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
* DONE (BiocParallel)
BiocParallel.Rcheck/tests/test.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
cleaning registry...
cleaning registry...
cleaning registry...
cleaning registry...
Adding jobs ...
Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding jobs ...
Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
cleaning registry...
Adding jobs ...
Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ...
cleaning registry...
Adding jobs ...
Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding 5 jobs ...
Submitting 5 jobs in 2 chunks using cluster functions 'Interactive' ...
cleaning registry...
Adding 5 jobs ...
Submitting 5 jobs in 2 chunks using cluster functions 'Multicore' ...
> > > > > > > >
cleaning registry...
Adding 5 jobs ...
Submitting 5 jobs in 2 chunks using cluster functions 'Socket' ...
cleaning registry...
Adding 5 jobs ...
Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding 3 jobs ...
Submitting 3 jobs in 3 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding 3 jobs ...
Submitting 3 jobs in 2 chunks using cluster functions 'Interactive' ...
cleaning registry...
Adding 3 jobs ...
Submitting 3 jobs in 2 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding 3 jobs ...
Submitting 3 jobs in 2 chunks using cluster functions 'Socket' ...
cleaning registry...
Adding 2 jobs ...
Submitting 2 jobs in 2 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding 2 jobs ...
Submitting 2 jobs in 2 chunks using cluster functions 'Socket' ...
cleaning registry...
Adding 2 jobs ...
Submitting 2 jobs in 2 chunks using cluster functions 'Multicore' ...
cleaning registry...
Adding 2 jobs ...
Submitting 2 jobs in 2 chunks using cluster functions 'Socket' ...
cleaning registry...
cleaning registry...
Timing stopped at: 0 0 0.001
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
Timing stopped at: 0.205 0.023 0.264
Error in DEACTIVATED("MPI tests not run") : MPI tests not run
> > test_bpiterate_Params
chunks greater than number of workers
ith param
ith param
ith param
chunks less than number of workers [1]
ith param
ith param
ith param
chunks less than number of workers [2]
ith param
ith param
cleanup
test_bpiterate_Params DONE
test_bpiterate_REDUCE
setup
ith param
no REDUCE
REDUCE
'reduce.in.order' FALSE [1]
'reduce.in.order' FALSE [2]
'reduce.in.order' TRUE [1]
'reduce.in.order' TRUE [2]
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Error in summary.connection(connection) : invalid connection
Calls: <Anonymous> ... sendData.SOCKnode -> serialize -> summary -> summary.connection
Timing stopped at: 0.306 0.118 16.65
Error : failed to stop 'SOCKcluster' cluster: invalid connection
test_bplapply_Params
setup
sqrt
serial
snow
dopar
batchjobs
mc
empty input
serial
snow
dopar
batchjobs
mc
BatchJobs
cleanup
test_bplapply_Params DONE
test_bplapply_symbols
setup
serial
snow
dopar
mc
cleanup
test_bplapply_symbols DONE
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
resuming previous calculation ...
RUNIT TEST PROTOCOL -- Mon Apr 15 22:42:23 2019
***********************************************
Number of test functions: 64
Number of deactivated test functions: 2
Number of errors: 1
Number of failures: 0
1 Test Suite :
BiocParallel RUnit Tests - 64 test functions, 1 error, 0 failures
DEACTIVATED test_SnowParam_MPI: MPI tests not run
DEACTIVATED test_SnowParam_coerce_from_MPI: MPI tests not run
ERROR in test_bpiterate_REDUCE: Error : failed to stop 'SOCKcluster' cluster: invalid connection
Test files with failing tests
test_SnowParam.R
test_SnowParam_MPI
test_SnowParam_coerce_from_MPI
test_bpiterate.R
test_bpiterate_REDUCE
Error in BiocGenerics:::testPackage("BiocParallel") :
unit tests failed for package BiocParallel
Execution halted
Error: failed to stop 'SOCKcluster' cluster: invalid connection
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: local ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
BiocParallel.Rcheck/BiocParallel-Ex.timings
| name | user | system | elapsed | |
| BatchJobsParam-class | 3.270 | 0.101 | 3.432 | |
| BatchtoolsParam-class | 5.265 | 3.833 | 11.403 | |
| BiocParallelParam-class | 0.002 | 0.000 | 0.003 | |
| DoparParam-class | 0.001 | 0.000 | 0.001 | |
| MulticoreParam-class | 0.825 | 0.457 | 2.608 | |
| SerialParam-class | 0.027 | 0.025 | 0.028 | |
| SnowParam-class | 0.398 | 0.065 | 5.995 | |
| bpaggregate | 7.932 | 0.498 | 8.373 | |
| bpiterate | 0.001 | 0.001 | 0.002 | |
| bplapply | 0.049 | 0.038 | 0.134 | |
| bploop | 0.000 | 0.001 | 0.001 | |
| bpmapply | 0.078 | 0.110 | 0.122 | |
| bpok | 0.144 | 0.068 | 9.014 | |
| bpschedule | 0.143 | 0.163 | 0.332 | |
| bptry | 0.196 | 0.323 | 0.313 | |
| bpvalidate | 0.307 | 0.111 | 0.355 | |
| bpvec | 0.745 | 0.294 | 0.907 | |
| bpvectorize | 0.052 | 0.049 | 0.144 | |
| ipcmutex | 0.186 | 0.242 | 5.254 | |
| register | 0.166 | 0.171 | 0.299 | |