BioC 3.5: CHECK report for GENE.E on malbec2

Package: GENE.E

Version: 1.15.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GENE.E_1.15.0.tar.gz

StartedAt: 2016-10-31 22:59:57 -0400 (Mon, 31 Oct 2016)

EndedAt: 2016-10-31 23:00:20 -0400 (Mon, 31 Oct 2016)

EllapsedTime: 23.7 seconds

RetCode: 0

Status:  OK

CheckDir: GENE.E.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GENE.E_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GENE.E.Rcheck’
* using R Under development (unstable) (2016-09-29 r71410)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GENE.E/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GENE.E’ version ‘1.15.0’
* 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 ... 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 ‘GENE.E’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rhdf5’ ‘RCurl’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rhdf5’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RCurl’ ‘rhdf5’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
from.genee: no visible global function definition for ‘download.file’
r2atr: no visible global function definition for ‘h5createGroup’
r2atr: no visible global function definition for ‘h5write’
read.gctx: no visible global function definition for ‘h5read’
read.meta: no visible global function definition for ‘h5read’
to.genee: no visible global function definition for ‘postForm’
to.genee: no visible global function definition for ‘fileUpload’
write.gctx: no visible global function definition for ‘h5createFile’
write.gctx: no visible global function definition for ‘h5createGroup’
write.gctx: no visible global function definition for ‘h5write’
write.meta: no visible global function definition for ‘h5write’
Undefined global functions or variables:
  download.file fileUpload h5createFile h5createGroup h5read h5write
  postForm
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GENE.E.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
from.genee	0	0	0
to.genee	0	0	0