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BioC 2.14: CHECK report for genomes on morelia

This page was generated on 2014-10-08 09:04:20 -0700 (Wed, 08 Oct 2014).

Package 335/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomes 2.10.0
Chris Stubben
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/genomes
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 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: genomes
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.10.0.tar.gz
StartedAt: 2014-10-07 23:03:30 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:06:09 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 159.1 seconds
RetCode: 0
Status:  OK 
CheckDir: genomes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/genomes.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘2.10.0’
* 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 ... [13s/13s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/26s] 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

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:

nameusersystemelapsed
doublingTime1.1480.0201.168
efetch0.0010.0000.001
einfo0.0010.0000.001
elink0.0010.0000.001
ena0.0010.0000.001
enaParse0.0000.0000.001
esearch0.0010.0000.001
esummary0.0010.0000.001
euks0.1120.0090.121
ftpList0.0000.0010.001
genomes-lines0.8670.0260.896
genomes-plot0.6220.0170.640
genomes-print0.2620.0130.275
genomes-summary0.0500.0070.058
genomes-update0.0030.0010.004
genomes0.630.020.65
genus0.5660.0150.582
image20.6700.0190.690
like0.6400.0130.655
ncbiGenome0.0000.0010.001
ncbiNucleotide0.0010.0000.001
ncbiProject0.0010.0000.001
ncbiPubmed0.0000.0010.000
ncbiRelease0.0160.0011.245
ncbiSubmit0.0010.0000.001
ncbiTaxonomy0.0010.0000.002
plotby0.8590.0200.879
proks0.7870.0260.815
read.genemark0.1610.0061.260
read.gff0.0750.0280.737
read.glimmer0.2340.0051.190
read.ncbi.ftp0.0010.0000.001
read.prodigal1.4832.6854.751
read.ptt0.5640.9172.303
species0.9710.0221.001
table20.0400.0040.043
virus0.1200.0050.125
year0.3220.0100.333