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BioC 3.5: CHECK report for FamAgg on oaxaca

This page was generated on 2017-03-04 16:51:02 -0500 (Sat, 04 Mar 2017).

Package 413/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FamAgg 1.3.3
Johannes Rainer
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FamAgg
Last Changed Rev: 125775 / Revision: 127142
Last Changed Date: 2017-01-09 04:31:20 -0500 (Mon, 09 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: FamAgg
Version: 1.3.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FamAgg_1.3.3.tar.gz
StartedAt: 2017-03-04 02:39:57 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 02:42:29 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 152.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FamAgg.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FamAgg_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/FamAgg.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FamAgg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FamAgg’ version ‘1.3.3’
* 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 ‘FamAgg’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::colMeans’ by ‘Matrix::colMeans’ when loading ‘FamAgg’
  Warning: replacing previous import ‘BiocGenerics::colSums’ by ‘Matrix::colSums’ when loading ‘FamAgg’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/FamAgg.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 ... 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
Examples with CPU or elapsed time > 5s
                user system elapsed
FAProbResults 10.673  0.688  11.393
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/FamAgg.Rcheck/00check.log’
for details.


FamAgg.Rcheck/00install.out:

* installing *source* package ‘FamAgg’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::colMeans’ by ‘Matrix::colMeans’ when loading ‘FamAgg’
Warning: replacing previous import ‘BiocGenerics::colSums’ by ‘Matrix::colSums’ when loading ‘FamAgg’
Creating a new generic function for ‘pedigree’ in package ‘FamAgg’
in method for ‘countGenerations’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘countGenerations’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘estimateGenerations’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘estimateGenerations’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘findFounders’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘findFounders’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘generationsFrom’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘generationsFrom’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getAncestors’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getAncestors’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getChildren’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getChildren’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getCommonAncestor’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getCommonAncestor’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getMissingMate’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getMissingMate’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getSiblings’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getSiblings’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getAll’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getAll’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getExternalMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getExternalMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getGenerationMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getGenerationMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getGenerationSexMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getGenerationSexMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getSexMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getSexMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::colMeans’ by ‘Matrix::colMeans’ when loading ‘FamAgg’
Warning: replacing previous import ‘BiocGenerics::colSums’ by ‘Matrix::colSums’ when loading ‘FamAgg’
* DONE (FamAgg)

FamAgg.Rcheck/FamAgg-Ex.timings:

nameusersystemelapsed
FAData-analysis2.5730.0412.704
FAData3.0830.0393.141
FAGenIndexResults1.0890.0191.110
FAIncidenceRateResults0.4510.0090.461
FAKinGroupResults3.3130.0303.403
FAKinSumResults1.0700.0131.085
FAProbResults10.673 0.68811.393
FAStdIncidenceRateResults0.3120.0240.336
Pedigree-utils1.5290.0121.546
defineControls0.1650.0060.171
plotting-functions0.0830.0040.092