BiocParallel 1.5.0
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf BiocParallel.buildbin-libdir BiocParallel.Rcheck && mkdir BiocParallel.buildbin-libdir BiocParallel.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.5.0.tar.gz >BiocParallel.Rcheck\00install.out 2>&1 && cp BiocParallel.Rcheck\00install.out BiocParallel-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BiocParallel.buildbin-libdir --install="check:BiocParallel-install.out" --force-multiarch --no-vignettes --timings BiocParallel_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/BiocParallel.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.5.0'
* 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 ... NOTE
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: no visible global function definition for
'clusterSetRNGStream'
bpstart,SnowParam: 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'
Undefined global functions or variables:
%dopar% batchMap buffer closeNode clusterExport clusterSetRNGStream
conditionmessage foreach getConfig getDoParName getDoParRegistered
getDoParWorkers id loadResults makeMPImaster mcexit mcfork
mpi.comm.disconnect mpi.comm.get.parent mpi.comm.set.errhandler
mpi.intercomm.merge mpi.quit setConfig sout submitJobs success
waitForJobs
* 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' ... [24s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpaggregate 3.48 0.1 8.59
** running examples for arch 'x64' ... [27s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpaggregate 4.03 0.11 8.97
SnowParam-class 0.14 0.00 5.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R' [35s]
[36s] OK
** running tests for arch 'x64' ...
Running 'test.R' [40s]
[40s] 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
'c:/biocbld/bbs-3.3-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.
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_1.5.0.zip
* DONE (BiocParallel)