BioC 3.2: CHECK report for goseq on linux1.bioconductor.org
This page was generated on 2015-10-27 17:24:37 -0400 (Tue, 27 Oct 2015).
goseq 1.22.0 Nadia Davidson
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/goseq | 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 | OK | OK | [ OK ] | |  |
windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: goseq |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings goseq_1.22.0.tar.gz |
StartedAt: 2015-10-27 04:14:40 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 04:18:18 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 217.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: goseq.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings goseq_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/goseq.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 ‘goseq/DESCRIPTION’ ... OK
* this is package ‘goseq’ version ‘1.22.0’
* 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 ‘goseq’ can be installed ... [19s/19s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘rtracklayer’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getgo: no visible global function definition for ‘toTable’
getlength: no visible global function definition for ‘toTable’
getlength: no visible global function definition for
‘transcriptLengths’
getlength: no visible global function definition for ‘browserSession’
getlength: no visible global function definition for ‘genome<-’
getlength: no visible global function definition for ‘ucscTableQuery’
getlength: no visible global function definition for ‘getTable’
* 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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
goseq 22.157 0.276 22.433
getgo 13.830 0.376 14.214
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/goseq.Rcheck/00check.log’
for details.
goseq.Rcheck/00install.out:
* installing *source* package ‘goseq’ ...
** 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 (goseq)
goseq.Rcheck/goseq-Ex.timings:
name | user | system | elapsed
|
genes | 0.017 | 0.000 | 0.017 |
|
getgo | 13.830 | 0.376 | 14.214 |
|
getlength | 2.909 | 0.108 | 3.080 |
|
goseq | 22.157 | 0.276 | 22.433 |
|
makespline | 0.041 | 0.000 | 0.041 |
|
nullp | 3.693 | 0.052 | 3.745 |
|
plotPWF | 3.232 | 0.064 | 3.296 |
|