BiocParallel 1.2.22
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/BiocParallel | | Last Changed Rev: 108966 / Revision: 109384 | | Last Changed Date: 2015-09-29 12:01:59 -0700 (Tue, 29 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocParallel_1.2.22.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/BiocParallel.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.22’
* 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 ... [4s/4s] 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:::.check_ncores’
‘parallel:::addClusterOptions’ ‘parallel:::checkCluster’
‘parallel:::children’ ‘parallel:::closeStdout’
‘parallel:::getClusterOption’ ‘parallel:::isChild’
‘parallel:::mc.advance.stream’ ‘parallel:::mc.set.stream’
‘parallel:::mcexit’ ‘parallel:::mcfork’ ‘parallel:::mckill’
‘parallel:::processID’ ‘parallel:::readChild’ ‘parallel:::recvData’
‘parallel:::recvOneData’ ‘parallel:::selectChildren’
‘parallel:::sendCall’ ‘parallel:::sendData’ ‘parallel:::sendMaster’
‘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
.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: 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/60s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bpvec 7.036 3.792 0.508
bpaggregate 9.036 1.213 9.017
bpmapply 5.503 3.612 1.309
MulticoreParam-class 2.768 1.221 9.487
SnowParam-class 0.315 0.081 20.211
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [98s/171s]
[98s/172s] 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.