BioC 3.6: CHECK report for BiocParallel on malbec1

Package: BiocParallel

Version: 1.11.6

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.11.6.tar.gz

StartedAt: 2017-08-15 21:33:53 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:36:24 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 151.2 seconds

RetCode: 0

Status:  OK

CheckDir: BiocParallel.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_1.11.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BiocParallel.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.11.6’
* 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
--------------------------------------------------------------------------
[[9698,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec1

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘BiocParallel/libs/BiocParallel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ipcmutex.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bpaggregate     6.208  0.208   6.535
SnowParam-class 0.404  0.084   5.350
ipcmutex        0.012  0.124   5.247
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 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-3.6-bioc/meat/BiocParallel.Rcheck/00check.log’
for details.

* installing *source* package ‘BiocParallel’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c ipcmutex.cpp -o ipcmutex.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/BiocParallel.Rcheck/BiocParallel/libs
** 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	3.372	0.048	3.511
BiocParallelParam-class	0.000	0.000	0.002
DoparParam-class	0	0	0
MulticoreParam-class	0.532	0.100	2.681
SerialParam-class	0.012	0.000	0.012
SnowParam-class	0.404	0.084	5.350
bpaggregate	6.208	0.208	6.535
bpiterate	0.004	0.000	0.004
bplapply	0.012	0.032	0.094
bploop	0	0	0
bpmapply	0.028	0.068	0.148
bpok	0.064	0.112	2.440
bpschedule	0.036	0.056	0.148
bptry	0.032	0.120	0.260
bpvalidate	0.376	0.012	0.390
bpvec	0.528	0.092	0.678
bpvectorize	0.028	0.048	0.137
ipcmutex	0.012	0.124	5.247
register	0.048	0.068	0.243