BioC 3.4: CHECK report for HDF5Array on malbec1

Package: HDF5Array

Version: 1.2.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HDF5Array_1.2.1.tar.gz

StartedAt: 2017-04-14 23:09:17 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:14:16 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 298.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HDF5Array.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HDF5Array_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/HDF5Array.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.2.1’
* package encoding: UTF-8
* 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 ‘HDF5Array’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
* checking package 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:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::combine_dimnames’
  ‘IRanges:::combine_dimnames_along’ ‘IRanges:::combine_dims_along’
  ‘IRanges:::get_dims_to_bind’ ‘IRanges:::simple_abind’
  ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::sapply_isNULL’
  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 ... WARNING
Undocumented S4 methods:
  generic 'dlogis' and siglist 'DelayedArray'
  generic 'plogis' and siglist 'DelayedArray'
  generic 'qlogis' and siglist 'DelayedArray'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.

* installing *source* package ‘HDF5Array’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘apply’ in package ‘HDF5Array’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘HDF5Array’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘HDF5Array’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘HDF5Array’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (HDF5Array)

name	user	system	elapsed
DelayedArray-class	2.472	0.048	2.520
DelayedArray-utils	1.748	0.052	1.803
HDF5Array-class	4.376	0.184	4.564
cbind-methods	0.996	0.060	1.058
setHDF5DumpFile	0.408	0.000	0.408