BioC 3.3: CHECK report for BiocParallel on linux2.bioconductor.org

Package: BiocParallel

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.5.0.tar.gz

StartedAt: 2015-10-27 02:02:54 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:05:14 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 139.5 seconds

RetCode: 0

Status:  OK

CheckDir: BiocParallel.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/BiocParallel.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BiocParallel’ can be installed ... [2s/1s] 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
.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 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 ... [20s/23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bpaggregate     4.443  0.108   5.245
SnowParam-class 0.330  0.087   6.018
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [55s/95s]
 [55s/96s] 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-3.3-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.

* 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
* DONE (BiocParallel)

name	user	system	elapsed
BatchJobsParam-class	1.744	0.040	1.785
BiocParallelParam-class	0.002	0.000	0.002
DoparParam-class	0.001	0.000	0.001
MulticoreParam-class	1.238	0.234	3.322
SerialParam-class	0.451	0.069	0.006
SnowParam-class	0.330	0.087	6.018
bpaggregate	4.443	0.108	5.245
bpiterate	0.003	0.000	0.002
bplapply	0.546	0.180	0.957
bpmapply	1.119	0.326	0.057
bpok	0.044	0.071	2.405
bpschedule	0.027	0.043	0.717
bpvalidate	1.086	0.279	0.153
bpvec	3.341	0.810	0.258
bpvectorize	0.008	0.022	0.015
register	1.580	0.509	1.852