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BioC 3.6: CHECK report for DelayedArray on veracruz1

This page was generated on 2017-08-16 13:49:46 -0400 (Wed, 16 Aug 2017).

Package 336/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DelayedArray 0.3.19
Hervé Pagès
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DelayedArray
Last Changed Rev: 131615 / Revision: 131943
Last Changed Date: 2017-07-27 09:41:52 -0400 (Thu, 27 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DelayedArray
Version: 0.3.19
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DelayedArray_0.3.19.tar.gz
StartedAt: 2017-08-16 02:07:21 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:17:02 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 580.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: DelayedArray.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DelayedArray_0.3.19.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DelayedArray.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DelayedArray/DESCRIPTION’ ... OK
* this is package ‘DelayedArray’ version ‘0.3.19’
* 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 ‘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
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:::anyMissing’ ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::diffWithInitialZero’
  ‘S4Vectors:::extract_positions_from_Rle’ ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
DelayedArray-utils 5.259   0.60   6.018
DelayedArray-class 4.970   0.15   5.326
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/DelayedArray.Rcheck/00check.log’
for details.


DelayedArray.Rcheck/00install.out:

* installing *source* package ‘DelayedArray’ ...
** R
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"DelayedMatrix","dgCMatrix"’: no definition for class “dgCMatrix”
in method for ‘coerce’ with signature ‘"DelayedMatrix","sparseMatrix"’: no definition for class “sparseMatrix”
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
** installing vignettes
** testing if installed package can be loaded
* DONE (DelayedArray)

DelayedArray.Rcheck/DelayedArray-Ex.timings:

nameusersystemelapsed
Array-class0.0010.0000.001
ArrayGrid-class0.3950.0090.423
DelayedArray-class4.9700.1505.326
DelayedArray-utils5.2590.6006.018
RleArray-class1.0850.0541.161
cbind-methods0.7820.0770.893
realize2.4940.2702.844