BioC 2.13: CHECK report for genomes on zin1
This page was generated on 2014-04-05 09:47:55 -0700 (Sat, 05 Apr 2014).
genomes 2.8.0 Chris Stubben
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/genomes | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
Package: genomes |
Version: 2.8.0 |
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.8.0.tar.gz |
StartedAt: 2014-04-05 01:25:26 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 01:27:35 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 128.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: genomes.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/genomes.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomes’ version ‘2.8.0’
* 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 ‘genomes’ can be installed ... [10s/10s] 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘genome-tables.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [16s/23s] 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
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/genomes.Rcheck/00check.log’
for details.
genomes.Rcheck/00install.out:
* installing *source* package ‘genomes’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genomes)
genomes.Rcheck/genomes-Ex.timings:
name | user | system | elapsed
|
doublingTime | 0.928 | 0.004 | 0.933 |
|
efetch | 0.012 | 0.000 | 0.012 |
|
einfo | 0.008 | 0.000 | 0.009 |
|
elink | 0.012 | 0.000 | 0.013 |
|
ena | 0.008 | 0.000 | 0.009 |
|
enaParse | 0.008 | 0.000 | 0.009 |
|
esearch | 0.008 | 0.000 | 0.008 |
|
esummary | 0.164 | 0.000 | 0.162 |
|
euks | 0.092 | 0.000 | 0.093 |
|
ftpList | 0.004 | 0.000 | 0.003 |
|
genomes-lines | 0.548 | 0.004 | 0.553 |
|
genomes-plot | 0.516 | 0.000 | 0.517 |
|
genomes-print | 0.384 | 0.004 | 0.389 |
|
genomes-summary | 0.052 | 0.000 | 0.054 |
|
genomes-update | 0.012 | 0.000 | 0.012 |
|
genomes | 0.552 | 0.000 | 0.552 |
|
genus | 0.664 | 0.004 | 0.670 |
|
image2 | 0.720 | 0.004 | 0.724 |
|
like | 0.532 | 0.000 | 0.531 |
|
ncbiGenome | 0.008 | 0.000 | 0.007 |
|
ncbiNucleotide | 0.032 | 0.004 | 0.470 |
|
ncbiProject | 0.008 | 0.000 | 0.006 |
|
ncbiPubmed | 0.004 | 0.000 | 0.006 |
|
ncbiRelease | 0.016 | 0.004 | 1.282 |
|
ncbiSubmit | 0.008 | 0.000 | 0.007 |
|
ncbiTaxonomy | 0.004 | 0.000 | 0.007 |
|
plotby | 0.632 | 0.020 | 0.652 |
|
proks | 0.776 | 0.004 | 0.791 |
|
read.genemark | 0.124 | 0.000 | 1.102 |
|
read.gff | 0.068 | 0.008 | 0.712 |
|
read.glimmer | 0.160 | 0.008 | 1.161 |
|
read.ncbi.ftp | 0.008 | 0.000 | 0.007 |
|
read.prodigal | 0.812 | 0.808 | 2.510 |
|
read.ptt | 0.340 | 0.272 | 1.669 |
|
species | 0.816 | 0.004 | 0.821 |
|
table2 | 0.044 | 0.000 | 0.046 |
|
virus | 0.104 | 0.000 | 0.102 |
|
year | 0.256 | 0.000 | 0.259 |
|