BioC 3.2: CHECK report for genomes on linux1.bioconductor.org
This page was generated on 2015-10-27 17:24:38 -0400 (Tue, 27 Oct 2015).
genomes 2.16.0
Chris Stubben
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/genomes | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: genomes |
| Version: 2.16.0 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.16.0.tar.gz |
| StartedAt: 2015-10-27 03:54:35 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 03:56:24 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 108.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genomes.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/genomes.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 ‘genomes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomes’ version ‘2.16.0’
* 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 ... [9s/9s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/19s] 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-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 | 1.670 | 0.032 | 1.706 |
|
| efetch | 0.001 | 0.000 | 0.001 |
|
| einfo | 0.001 | 0.000 | 0.001 |
|
| elink | 0.001 | 0.000 | 0.001 |
|
| esearch | 0.001 | 0.000 | 0.000 |
|
| esummary | 0.001 | 0.000 | 0.001 |
|
| euks | 0.091 | 0.000 | 0.091 |
|
| ftpList | 0.001 | 0.000 | 0.001 |
|
| genomes-lines | 0.920 | 0.011 | 0.937 |
|
| genomes-plot | 0.553 | 0.004 | 0.561 |
|
| genomes-print | 0.299 | 0.008 | 0.306 |
|
| genomes-summary | 0.025 | 0.000 | 0.025 |
|
| genomes-update | 0.001 | 0.000 | 0.001 |
|
| genomes | 0.596 | 0.004 | 0.599 |
|
| genus | 0.744 | 0.000 | 0.745 |
|
| image2 | 0.592 | 0.008 | 0.600 |
|
| like | 0.465 | 0.004 | 0.469 |
|
| ncbiGenome | 0.000 | 0.000 | 0.001 |
|
| ncbiNucleotide | 0 | 0 | 0 |
|
| ncbiProject | 0.001 | 0.000 | 0.000 |
|
| ncbiPubmed | 0.001 | 0.000 | 0.000 |
|
| ncbiRelease | 0.010 | 0.001 | 1.159 |
|
| ncbiSubmit | 0 | 0 | 0 |
|
| ncbiTaxonomy | 0.000 | 0.000 | 0.001 |
|
| plotby | 1.155 | 0.000 | 1.155 |
|
| proks | 1.104 | 0.004 | 1.108 |
|
| read.genemark | 0.072 | 0.000 | 0.206 |
|
| read.gff | 0.025 | 0.012 | 0.132 |
|
| read.glimmer | 0.093 | 0.007 | 0.389 |
|
| read.ncbi.ftp | 0.001 | 0.000 | 0.001 |
|
| read.prodigal | 0.790 | 1.236 | 2.143 |
|
| read.ptt | 0.155 | 0.288 | 0.536 |
|
| species | 0.803 | 0.000 | 0.802 |
|
| table2 | 0.015 | 0.008 | 0.024 |
|
| virus | 0.064 | 0.000 | 0.064 |
|
| year | 0.327 | 0.004 | 0.331 |
|