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BioC 3.3: CHECK report for genotypeeval on morelia

This page was generated on 2016-04-21 13:26:51 -0700 (Thu, 21 Apr 2016).

Package 474/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genotypeeval 1.1.0
Jennifer Tom
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genotypeeval
Last Changed Rev: 109592 / Revision: 116626
Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: genotypeeval
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genotypeeval_1.1.0.tar.gz
StartedAt: 2016-04-21 03:05:29 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 03:10:05 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 276.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genotypeeval.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 genotypeeval_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/genotypeeval.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genotypeeval/DESCRIPTION’ ... OK
* this is package ‘genotypeeval’ version ‘1.1.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genotypeeval’ can be installed ... [22s/22s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘genotypeeval’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/genotypeeval.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 ... NOTE
ReadVCFDataChunk: no visible global function definition for
  ‘read.table’
getCoefs: no visible global function definition for ‘constrOptim’
Undefined global functions or variables:
  constrOptim read.table
Consider adding
  importFrom("stats", "constrOptim")
  importFrom("utils", "read.table")
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 ... [51s/51s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getPlots         5.918  0.201   6.155
ReadVCFDataChunk 5.385  0.365   5.769
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [18s/18s]
 [18s/18s] 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-3.3-bioc/meat/genotypeeval.Rcheck/00check.log’
for details.


genotypeeval.Rcheck/00install.out:

* installing *source* package ‘genotypeeval’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘genotypeeval’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘genotypeeval’
* DONE (genotypeeval)

genotypeeval.Rcheck/genotypeeval-Ex.timings:

nameusersystemelapsed
GoldDataFromGRanges0.0690.0000.069
GoldDataParam0.0010.0000.001
ReadGoldData0.6330.0320.687
ReadVCFData3.4610.1583.633
ReadVCFDataChunk5.3850.3655.769
VCFEvaluate4.4870.2294.756
VCFQAParam0.0020.0000.002
didSamplePass4.1940.2124.434
didSamplePassOverall3.2410.1823.433
getName3.6650.1813.858
getPlots5.9180.2016.155
getResults4.5000.2054.754
getVR2.7790.1983.059