| Back to the "Multiple platform build/check report" | A [B] C D E F G H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2015-08-20 13:21:15 -0700 (Thu, 20 Aug 2015).
| Package 98/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| BiocParallel 1.3.50 Bioconductor Package Maintainer
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | |||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK | ||||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BiocParallel |
| Version: 1.3.50 |
| Command: rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.3.50.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.3.50.tar.gz |
| StartedAt: 2015-08-20 01:51:35 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 01:56:46 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 311.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BiocParallel.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.3.50.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.3.50.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/BiocParallel.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocParallel/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocParallel' version '1.3.50'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'library' or 'require' call not declared from: 'futile.logger'
'library' or 'require' call to 'futile.logger' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
'BatchJobs:::checkDir' 'parallel:::.check_ncores'
'parallel:::addClusterOptions' 'parallel:::checkCluster'
'parallel:::getClusterOption' 'parallel:::recvData'
'parallel:::recvOneData' 'parallel:::sendCall' 'parallel:::sendData'
'parallel:::sinkWorkerOutput'
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 ... NOTE
.bpnewForkNode: no visible global function definition for 'mcfork'
.bpnewForkNode: no visible global function definition for 'mcexit'
.clear_cluster : <anonymous>: no visible global function definition for
'conditionmessage'
.initiateLogging: no visible global function definition for
'clusterExport'
.initiateLogging : .bufferload : fun: no visible binding for '<<-'
assignment to 'buffer'
.initiateLogging : .bufferload : fun: no visible binding for global
variable 'buffer'
.try : handler_error: no visible binding for '<<-' assignment to
'success'
.try_log : handler_error: no visible binding for '<<-' assignment to
'success'
bprunMPIslave: no visible global function definition for
'mpi.comm.get.parent'
bprunMPIslave: no visible global function definition for
'mpi.intercomm.merge'
bprunMPIslave: no visible global function definition for
'mpi.comm.set.errhandler'
bprunMPIslave: no visible global function definition for
'mpi.comm.disconnect'
bprunMPIslave: no visible global function definition for
'makeMPImaster'
bprunMPIslave: no visible global function definition for 'mpi.quit'
bpslaveLoop: no visible binding for '<<-' assignment to 'buffer'
bpslaveLoop: no visible binding for '<<-' assignment to 'success'
bpslaveLoop: no visible global function definition for 'closeNode'
bpslaveLoop : handler: no visible binding for '<<-' assignment to
'success'
bpslaveLoop: no visible binding for global variable 'success'
bpslaveLoop: no visible binding for global variable 'buffer'
bpslaveLoop: no visible binding for global variable 'sout'
bpbackend,BatchJobsParam: no visible global function definition for
'getConfig'
bpisup,DoparParam: no visible global function definition for
'getDoParRegistered'
bpisup,DoparParam: no visible global function definition for
'getDoParName'
bpisup,DoparParam: no visible global function definition for
'getDoParWorkers'
bplapply,ANY-BatchJobsParam: no visible global function definition for
'getConfig'
bplapply,ANY-BatchJobsParam: no visible global function definition for
'setConfig'
bplapply,ANY-BatchJobsParam: no visible global function definition for
'batchMap'
bplapply,ANY-BatchJobsParam: no visible binding for global variable
'submitJobs'
bplapply,ANY-BatchJobsParam: no visible global function definition for
'waitForJobs'
bplapply,ANY-BatchJobsParam: no visible global function definition for
'loadResults'
bplapply,ANY-DoparParam: no visible global function definition for
'%dopar%'
bplapply,ANY-DoparParam: no visible global function definition for
'foreach'
bpstart,SnowParam : .local: no visible global function definition for
'clusterSetRNGStream'
bpstart,SnowParam : .local: no visible global function definition for
'clusterExport'
bpvec,ANY-MulticoreParam: no visible binding for global variable 'id'
bpworkers,DoparParam: no visible global function definition for
'getDoParWorkers'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [45s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpaggregate 6.77 0.07 16.72
SnowParam-class 0.15 0.03 7.97
bplapply 0.12 0.05 6.46
** running examples for arch 'x64' ... [50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpaggregate 7.70 0.16 19.82
SnowParam-class 0.17 0.01 8.88
bplapply 0.07 0.06 6.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R' [77s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "test.R" "test.Rout"' had status 1
ERROR
Running the tests in 'tests/test.R' failed.
Last 13 lines of output:
Test files with failing tests
test_bpmapply.R
test_bpmapply_Params
test_errorhandling.R
test_BPREDO
test_catching_errors
Error in BiocGenerics:::testPackage("BiocParallel") :
unit tests failed for package BiocParallel
Execution halted
** running tests for arch 'x64' ...
Running 'test.R' [85s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "test.R" "test.Rout"' had status 1
ERROR
Running the tests in 'tests/test.R' failed.
Last 13 lines of output:
Test files with failing tests
test_bpmapply.R
test_bpmapply_Params
test_errorhandling.R
test_BPREDO
test_catching_errors
Error in BiocGenerics:::testPackage("BiocParallel") :
unit tests failed for package BiocParallel
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: 2 ERRORs, 1 WARNING, 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.
BiocParallel.Rcheck/tests_i386/test.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
Sourcing configuration file: 'D:/biocbld/bbs-3.2-bioc/R/library/BatchJobs/etc/BatchJobs_global_config.R'
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
Syncing registry ...
Syncing registry ...
Syncing registry ...
Loading required package: snow
starting worker for localhost:11494
starting worker for localhost:11494
Warning in MulticoreParam(jobname = "test") :
MulticoreParam not supported on Windows. Use SnowParam instead.
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
Loading required package: foreach
Loading required package: iterators
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+++++ | 10% (00:00:00)
SubmitJobs |++++++++++ | 20% (00:00:00)
SubmitJobs |+++++++++++++++ | 30% (00:00:00)
SubmitJobs |++++++++++++++++++++ | 40% (00:00:01)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++ | 60% (00:00:00)
SubmitJobs |++++++++++++++++++++++++++++++++++ | 70% (00:00:00)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++ | 80% (00:00:00)
SubmitJobs |++++++++++++++++++++++++++++++++++++++++++++ | 90% (00:00:00)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:10 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:2 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
Timing stopped at: 0.08 0 1.8
Error in summary.connection(connection) : invalid connection
starting worker for localhost:11494
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:snow':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: Biostrings
Warning in bpvalidate(fun) : function references unknown symbol(s)
starting worker for localhost:11494
starting worker for localhost:11494
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:00)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:2 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
starting worker for localhost:11494
starting worker for localhost:11494
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:2 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Resuming previous calculation ...
Resuming previous calculation ...
starting worker for localhost:11494
starting worker for localhost:11494
Resuming previous calculation ...
starting worker for localhost:11494
Resuming previous calculation ...
starting worker for localhost:11494
Timing stopped at: 0.11 0.05 5.82
Error in summary.connection(connection) : invalid connection
starting worker for localhost:11494
starting worker for localhost:11494
ERROR [2015-08-20 01:55:05] hit error
starting worker for localhost:11494
starting worker for localhost:11494
Timing stopped at: 0.1 0.01 1.69
Error in summary.connection(connection) : invalid connection
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
starting worker for localhost:11494
loading futile.logger on workers
############### LOG OUTPUT ###############
Task: 1
Node: 1
Timestamp: 2015-08-20 01:55:10
Success: TRUE
Task duration:
user system elapsed
0.02 0.00 0.02
Memory used:
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 317735 8.5 592000 15.9 347722 9.3
Vcells 263683 2.1 786432 6.0 289809 2.3
Log messages:
stderr and stdout:
character(0)
############### LOG OUTPUT ###############
Task: 2
Node: 2
Timestamp: 2015-08-20 01:55:11
Success: FALSE
Task duration:
user system elapsed
0.04 0.00 0.03
Memory used:
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 327898 8.8 592000 15.9 386273 10.4
Vcells 274833 2.1 786432 6.0 384215 3.0
Log messages:
ERROR [2015-08-20 01:55:10] non-numeric argument to mathematical function
stderr and stdout:
character(0)
starting worker for localhost:11494
starting worker for localhost:11494
RUNIT TEST PROTOCOL -- Thu Aug 20 01:55:12 2015
***********************************************
Number of test functions: 25
Number of errors: 3
Number of failures: 0
1 Test Suite :
BiocParallel RUnit Tests - 25 test functions, 3 errors, 0 failures
ERROR in test_bpmapply_Params: Error in summary.connection(connection) : invalid connection
ERROR in test_BPREDO: Error in summary.connection(connection) : invalid connection
ERROR in test_catching_errors: Error in summary.connection(connection) : invalid connection
Test files with failing tests
test_bpmapply.R
test_bpmapply_Params
test_errorhandling.R
test_BPREDO
test_catching_errors
Error in BiocGenerics:::testPackage("BiocParallel") :
unit tests failed for package BiocParallel
Execution halted
BiocParallel.Rcheck/tests_x64/test.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Sourcing configuration file: 'D:/biocbld/bbs-3.2-bioc/R/library/BatchJobs/etc/BatchJobs_global_config.R'
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
Syncing registry ...
Syncing registry ...
Syncing registry ...
Loading required package: snow
starting worker for localhost:11906
starting worker for localhost:11906
Warning in MulticoreParam(jobname = "test") :
MulticoreParam not supported on Windows. Use SnowParam instead.
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
Loading required package: foreach
Loading required package: iterators
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+++++ | 10% (00:00:00)
SubmitJobs |++++++++++ | 20% (00:00:00)
SubmitJobs |+++++++++++++++ | 30% (00:00:00)
SubmitJobs |++++++++++++++++++++ | 40% (00:00:01)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++ | 60% (00:00:00)
SubmitJobs |++++++++++++++++++++++++++++++++++ | 70% (00:00:00)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++ | 80% (00:00:00)
SubmitJobs |++++++++++++++++++++++++++++++++++++++++++++ | 90% (00:00:00)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:10 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:2 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
Timing stopped at: 0.05 0 2.48
Error in summary.connection(connection) : invalid connection
starting worker for localhost:11906
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:snow':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parRapply, parSapply
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: Biostrings
Warning in bpvalidate(fun) : function references unknown symbol(s)
starting worker for localhost:11906
starting worker for localhost:11906
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:2 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
starting worker for localhost:11906
starting worker for localhost:11906
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |+ | 0% (00:00:00)
SubmitJobs |++++++++++++++++++++++++ | 50% (00:00:01)
SubmitJobs |+++++++++++++++++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Syncing registry ...
Waiting |+ | 0% (00:00:00)
Waiting [S:0 D:2 E:0 R:0] |++++++++++++++++++++++++++++++++++| 100% (00:00:00)
Resuming previous calculation ...
Resuming previous calculation ...
starting worker for localhost:11906
starting worker for localhost:11906
Resuming previous calculation ...
starting worker for localhost:11906
Resuming previous calculation ...
starting worker for localhost:11906
Timing stopped at: 0.1 0.01 6.32
Error in summary.connection(connection) : invalid connection
starting worker for localhost:11906
starting worker for localhost:11906
ERROR [2015-08-20 01:56:31] hit error
starting worker for localhost:11906
starting worker for localhost:11906
Timing stopped at: 0.05 0 1.98
Error in summary.connection(connection) : invalid connection
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
starting worker for localhost:11906
loading futile.logger on workers
############### LOG OUTPUT ###############
Task: 1
Node: 1
Timestamp: 2015-08-20 01:56:37
Success: TRUE
Task duration:
user system elapsed
0.01 0.00 0.02
Memory used:
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 317736 17.0 592000 31.7 347723 18.6
Vcells 421370 3.3 1023718 7.9 454059 3.5
Log messages:
stderr and stdout:
character(0)
############### LOG OUTPUT ###############
Task: 2
Node: 2
Timestamp: 2015-08-20 01:56:37
Success: FALSE
Task duration:
user system elapsed
0.03 0.00 0.03
Memory used:
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 327899 17.6 592000 31.7 386274 20.7
Vcells 440140 3.4 1023718 7.9 565627 4.4
Log messages:
ERROR [2015-08-20 01:56:37] non-numeric argument to mathematical function
stderr and stdout:
character(0)
starting worker for localhost:11906
starting worker for localhost:11906
RUNIT TEST PROTOCOL -- Thu Aug 20 01:56:38 2015
***********************************************
Number of test functions: 25
Number of errors: 3
Number of failures: 0
1 Test Suite :
BiocParallel RUnit Tests - 25 test functions, 3 errors, 0 failures
ERROR in test_bpmapply_Params: Error in summary.connection(connection) : invalid connection
ERROR in test_BPREDO: Error in summary.connection(connection) : invalid connection
ERROR in test_catching_errors: Error in summary.connection(connection) : invalid connection
Test files with failing tests
test_bpmapply.R
test_bpmapply_Params
test_errorhandling.R
test_BPREDO
test_catching_errors
Error in BiocGenerics:::testPackage("BiocParallel") :
unit tests failed for package BiocParallel
Execution halted
BiocParallel.Rcheck/00install.out:
install for i386 * installing *source* package 'BiocParallel' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'BiocParallel' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'BiocParallel' as BiocParallel_1.3.50.zip * DONE (BiocParallel)
BiocParallel.Rcheck/examples_i386/BiocParallel-Ex.timings:
| name | user | system | elapsed | |
| BatchJobsParam-class | 1.97 | 0.10 | 3.54 | |
| BiocParallelParam-class | 0 | 0 | 0 | |
| DoparParam-class | 0 | 0 | 0 | |
| MulticoreParam-class | 0.08 | 0.00 | 2.07 | |
| SerialParam-class | 0.02 | 0.00 | 0.02 | |
| SnowParam-class | 0.15 | 0.03 | 7.97 | |
| bpaggregate | 6.77 | 0.07 | 16.72 | |
| bpiterate | 0 | 0 | 0 | |
| bplapply | 0.12 | 0.05 | 6.46 | |
| bpmapply | 0 | 0 | 0 | |
| bpok | 0.11 | 0.00 | 2.50 | |
| bpschedule | 0.03 | 0.00 | 0.03 | |
| bpvalidate | 0.39 | 0.00 | 0.39 | |
| bpvec | 0.23 | 0.00 | 1.46 | |
| bpvectorize | 0.03 | 0.00 | 1.11 | |
| register | 0.05 | 0.00 | 1.67 | |
BiocParallel.Rcheck/examples_x64/BiocParallel-Ex.timings:
| name | user | system | elapsed | |
| BatchJobsParam-class | 2.67 | 0.08 | 2.99 | |
| BiocParallelParam-class | 0 | 0 | 0 | |
| DoparParam-class | 0 | 0 | 0 | |
| MulticoreParam-class | 0.09 | 0.00 | 2.10 | |
| SerialParam-class | 0.02 | 0.00 | 0.02 | |
| SnowParam-class | 0.17 | 0.01 | 8.88 | |
| bpaggregate | 7.70 | 0.16 | 19.82 | |
| bpiterate | 0.02 | 0.00 | 0.01 | |
| bplapply | 0.07 | 0.06 | 6.42 | |
| bpmapply | 0.02 | 0.00 | 0.01 | |
| bpok | 0.11 | 0.00 | 3.29 | |
| bpschedule | 0.02 | 0.00 | 0.01 | |
| bpvalidate | 0.44 | 0.00 | 0.44 | |
| bpvec | 0.34 | 0.02 | 2.12 | |
| bpvectorize | 0.02 | 0.00 | 1.24 | |
| register | 0.05 | 0.01 | 1.69 | |