BioC 3.1: CHECK report for SeqVarTools on zin2
This page was generated on 2015-10-09 09:25:39 -0700 (Fri, 09 Oct 2015).
SeqVarTools 1.6.0 Stephanie M. Gogarten , Xiuwen Zheng
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/SeqVarTools | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: SeqVarTools |
Version: 1.6.0 |
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SeqVarTools_1.6.0.tar.gz |
StartedAt: 2015-10-09 05:27:19 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 05:30:15 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 175.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SeqVarTools.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SeqVarTools_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/SeqVarTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqVarTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqVarTools’ version ‘1.6.0’
* 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 ‘SeqVarTools’ can be installed ... [14s/14s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘SeqArray:::.altAllele’ ‘SeqArray:::.refAllele’
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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [28s/28s]
[28s/28s] 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 NOTE
See
‘/home/biocbuild/bbs-3.1-bioc/meat/SeqVarTools.Rcheck/00check.log’
for details.
SeqVarTools.Rcheck/00install.out:
* installing *source* package ‘SeqVarTools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (SeqVarTools)
SeqVarTools.Rcheck/SeqVarTools-Ex.timings:
name | user | system | elapsed
|
allele-methods | 0.020 | 0.000 | 0.034 |
|
alleleFrequency | 0.383 | 0.000 | 0.383 |
|
applyMethod | 0.302 | 0.004 | 0.306 |
|
duplicateDiscordance | 0.017 | 0.000 | 0.016 |
|
getGenotype | 0.009 | 0.000 | 0.010 |
|
getVariableLengthData | 0.009 | 0.000 | 0.008 |
|
heterozygosity | 0.269 | 0.004 | 0.273 |
|
hwe | 0.117 | 0.000 | 0.117 |
|
inbreedCoeff | 0.214 | 0.000 | 0.214 |
|
isSNV | 0.004 | 0.000 | 0.004 |
|
isVariant | 0.004 | 0.000 | 0.005 |
|
meanBySample | 0.027 | 0.000 | 0.027 |
|
mendelErr | 0.023 | 0.000 | 0.026 |
|
missingGenotypeRate | 0.018 | 0.000 | 0.017 |
|
pca | 0.646 | 0.004 | 0.650 |
|
pedigree | 0.004 | 0.000 | 0.005 |
|
setVariantID | 0.010 | 0.000 | 0.009 |
|
titv | 0.45 | 0.00 | 0.45 |
|