BioC 2.14: CHECK report for HTSeqGenie on zin2

Package: HTSeqGenie

Version: 3.14.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings HTSeqGenie_3.14.1.tar.gz

StartedAt: 2014-10-08 00:26:58 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:36:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 572.4 seconds

RetCode: 0

Status:  OK

CheckDir: HTSeqGenie.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings HTSeqGenie_3.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/HTSeqGenie.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘3.14.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... [31s/32s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
writeToFile: no visible binding for global variable ‘logging.file’
* 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 ... [15s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [177s/250s]
 [177s/250s] 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

* installing *source* package ‘HTSeqGenie’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HTSeqGenie)

name	user	system	elapsed
HTSeqGenie	0.004	0.000	0.001
buildGenomicFeaturesFromTxDb	0.000	0.000	0.001
runPipeline	0.004	0.000	0.002