BioC 3.1: CHECK report for genomes on petty
This page was generated on 2015-10-09 09:34:09 -0700 (Fri, 09 Oct 2015).
genomes 2.14.0 Chris Stubben
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/genomes | 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: genomes |
Version: 2.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomes_2.14.0.tar.gz |
StartedAt: 2015-10-08 23:15:26 -0700 (Thu, 08 Oct 2015) |
EndedAt: 2015-10-08 23:18:55 -0700 (Thu, 08 Oct 2015) |
EllapsedTime: 208.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: genomes.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomes_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/genomes.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.14.0’
* 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 ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
read.genemark: no visible global function definition for ‘isCircular<-’
read.genemark: no visible global function definition for ‘seqlengths<-’
read.genemark: no visible global function definition for ‘metadata<-’
read.gff: no visible global function definition for ‘seqlengths<-’
read.gff: no visible global function definition for ‘metadata<-’
read.glimmer: no visible global function definition for ‘isCircular<-’
read.glimmer: no visible global function definition for ‘seqlengths<-’
read.glimmer: no visible global function definition for ‘metadata<-’
read.ncbi.ftp : <anonymous>: no visible global function definition for
‘metadata’
read.ncbi.ftp: no visible global function definition for ‘seqlengths’
read.ncbi.ftp: no visible global function definition for ‘seqlevels<-’
read.ncbi.ftp: no visible global function definition for ‘seqlevels’
read.ncbi.ftp: no visible global function definition for ‘metadata<-’
read.prodigal: no visible global function definition for ‘isCircular<-’
read.prodigal: no visible global function definition for ‘seqlengths<-’
read.prodigal: no visible global function definition for ‘metadata<-’
read.ptt: no visible global function definition for ‘isCircular<-’
read.ptt: no visible global function definition for ‘seqlengths<-’
read.ptt: no visible global function definition for ‘metadata<-’
* 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 ... [35s/40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
read.prodigal 2.697 3.915 7.531
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/genomes.Rcheck/00check.log’
for details.
genomes.Rcheck/00install.out:
* installing *source* package ‘genomes’ ...
** R
** data
** 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 (genomes)
genomes.Rcheck/genomes-Ex.timings:
name | user | system | elapsed
|
doublingTime | 2.248 | 0.061 | 2.310 |
|
efetch | 0.001 | 0.000 | 0.001 |
|
einfo | 0.001 | 0.000 | 0.001 |
|
elink | 0.001 | 0.000 | 0.002 |
|
esearch | 0.001 | 0.000 | 0.002 |
|
esummary | 0.002 | 0.000 | 0.002 |
|
euks | 0.153 | 0.020 | 0.173 |
|
ftpList | 0.001 | 0.000 | 0.001 |
|
genomes-lines | 1.202 | 0.061 | 1.264 |
|
genomes-plot | 0.971 | 0.037 | 1.012 |
|
genomes-print | 0.549 | 0.025 | 0.574 |
|
genomes-summary | 0.037 | 0.013 | 0.051 |
|
genomes-update | 0.001 | 0.000 | 0.001 |
|
genomes | 1.099 | 0.031 | 1.129 |
|
genus | 1.166 | 0.028 | 1.197 |
|
image2 | 1.682 | 0.026 | 1.711 |
|
like | 1.060 | 0.037 | 1.097 |
|
ncbiGenome | 0.002 | 0.000 | 0.002 |
|
ncbiNucleotide | 0.002 | 0.001 | 0.002 |
|
ncbiProject | 0.001 | 0.000 | 0.001 |
|
ncbiPubmed | 0.001 | 0.001 | 0.001 |
|
ncbiRelease | 0.024 | 0.002 | 0.787 |
|
ncbiSubmit | 0.001 | 0.000 | 0.001 |
|
ncbiTaxonomy | 0.000 | 0.000 | 0.001 |
|
plotby | 1.905 | 0.041 | 1.948 |
|
proks | 1.659 | 0.049 | 1.711 |
|
read.genemark | 0.102 | 0.008 | 1.337 |
|
read.gff | 0.055 | 0.029 | 0.703 |
|
read.glimmer | 0.125 | 0.019 | 1.158 |
|
read.ncbi.ftp | 0.002 | 0.000 | 0.001 |
|
read.prodigal | 2.697 | 3.915 | 7.531 |
|
read.ptt | 1.964 | 1.336 | 4.163 |
|
species | 1.090 | 0.033 | 1.124 |
|
table2 | 0.418 | 0.019 | 0.438 |
|
virus | 0.187 | 0.009 | 0.195 |
|
year | 0.777 | 0.024 | 0.801 |
|