BioC 3.3: CHECK report for genomes on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:50 -0400 (Tue, 27 Oct 2015).
genomes 2.17.0 Chris Stubben
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genomes | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
Package: genomes |
Version: 2.17.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.17.0.tar.gz |
StartedAt: 2015-10-27 04:12:15 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 04:13:56 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 101.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: genomes.Rcheck |
Warnings: 0 |
Command output
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### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/genomes.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.17.0’
* 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 ... [8s/8s] 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<-’
Undefined global functions or variables:
isCircular<- metadata metadata<- seqlengths seqlengths<- seqlevels
seqlevels<-
* 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 ... [15s/18s] 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-3.3-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 | 1.326 | 0.028 | 1.355 |
|
efetch | 0.001 | 0.001 | 0.001 |
|
einfo | 0.001 | 0.000 | 0.000 |
|
elink | 0 | 0 | 0 |
|
esearch | 0.000 | 0.000 | 0.001 |
|
esummary | 0.001 | 0.000 | 0.001 |
|
euks | 0.224 | 0.001 | 0.228 |
|
ftpList | 0.001 | 0.000 | 0.001 |
|
genomes-lines | 0.446 | 0.004 | 0.449 |
|
genomes-plot | 0.585 | 0.004 | 0.589 |
|
genomes-print | 0.271 | 0.007 | 0.279 |
|
genomes-summary | 0.020 | 0.004 | 0.025 |
|
genomes-update | 0.001 | 0.000 | 0.001 |
|
genomes | 0.631 | 0.003 | 0.635 |
|
genus | 0.692 | 0.012 | 0.703 |
|
image2 | 1.062 | 0.005 | 1.067 |
|
like | 0.993 | 0.000 | 0.993 |
|
ncbiGenome | 0.000 | 0.000 | 0.001 |
|
ncbiNucleotide | 0.001 | 0.000 | 0.001 |
|
ncbiProject | 0.001 | 0.000 | 0.001 |
|
ncbiPubmed | 0.001 | 0.000 | 0.001 |
|
ncbiRelease | 0.016 | 0.000 | 0.784 |
|
ncbiSubmit | 0.001 | 0.000 | 0.001 |
|
ncbiTaxonomy | 0.000 | 0.000 | 0.001 |
|
plotby | 1.050 | 0.008 | 1.058 |
|
proks | 0.707 | 0.016 | 0.723 |
|
read.genemark | 0.040 | 0.004 | 0.185 |
|
read.gff | 0.019 | 0.004 | 0.394 |
|
read.glimmer | 0.059 | 0.004 | 0.575 |
|
read.ncbi.ftp | 0.001 | 0.000 | 0.001 |
|
read.prodigal | 0.783 | 1.112 | 2.179 |
|
read.ptt | 0.130 | 0.308 | 0.542 |
|
species | 0.589 | 0.008 | 0.597 |
|
table2 | 0.023 | 0.000 | 0.024 |
|
virus | 0.060 | 0.004 | 0.065 |
|
year | 0.341 | 0.000 | 0.341 |
|