BioC 3.5: CHECK report for DelayedArray on toluca2

Package: DelayedArray

Version: 0.1.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DelayedArray_0.1.11.tar.gz

StartedAt: 2017-04-23 02:50:39 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 03:02:32 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 712.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DelayedArray.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DelayedArray_0.1.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DelayedArray.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DelayedArray/DESCRIPTION’ ... OK
* this is package ‘DelayedArray’ version ‘0.1.11’
* 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 ‘DelayedArray’ can be installed ... OK
* checking installed package size ... OK
* 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
DelayedArray-utils 6.768  0.647   7.479
DelayedArray-class 5.218  0.131   5.374
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DelayedArray.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DelayedArray-class	5.218	0.131	5.374
DelayedArray-utils	6.768	0.647	7.479
RleArray-class	2.146	0.111	2.260
cbind-methods	0.729	0.084	0.813
realize	2.906	0.349	3.269