BioC 3.6: CHECK report for GOexpress on malbec1
This page was generated on 2017-08-16 13:22:23 -0400 (Wed, 16 Aug 2017).
GOexpress 1.11.0 Kevin Rue-Albrecht
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOexpress | Last Changed Rev: 129129 / Revision: 131943 | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | |
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: GOexpress |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.11.0.tar.gz |
StartedAt: 2017-08-15 23:38:48 -0400 (Tue, 15 Aug 2017) |
EndedAt: 2017-08-15 23:40:26 -0400 (Tue, 15 Aug 2017) |
EllapsedTime: 98.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GOexpress.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.11.0’
* 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 ‘GOexpress’ can be installed ... 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 ... NOTE
GO_analyse: no visible binding for global variable ‘microarray2dataset’
GO_analyse: no visible binding for global variable ‘prefix2dataset’
mart_from_ensembl: no visible binding for global variable
‘prefix2dataset’
Undefined global functions or variables:
microarray2dataset prefix2dataset
* 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 ... 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck/00check.log’
for details.
GOexpress.Rcheck/00install.out:
* installing *source* package ‘GOexpress’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOexpress)
GOexpress.Rcheck/GOexpress-Ex.timings:
name | user | system | elapsed
|
AlvMac | 0.128 | 0.004 | 0.129 |
|
AlvMac_GOgenes | 0.424 | 0.040 | 0.463 |
|
AlvMac_allGO | 0.020 | 0.000 | 0.022 |
|
AlvMac_allgenes | 0.012 | 0.000 | 0.013 |
|
AlvMac_results | 0.296 | 0.056 | 0.351 |
|
AlvMac_results.pVal | 2.828 | 0.356 | 3.187 |
|
GO_analyse | 2.644 | 0.052 | 2.698 |
|
GOexpress-package | 0.000 | 0.000 | 0.003 |
|
cluster_GO | 0.144 | 0.000 | 0.143 |
|
expression_plot | 2.904 | 0.000 | 2.902 |
|
expression_plot_symbol | 1.016 | 0.012 | 1.028 |
|
expression_profiles | 0.648 | 0.000 | 0.650 |
|
expression_profiles_symbol | 0.896 | 0.000 | 0.892 |
|
heatmap_GO | 1.188 | 0.024 | 1.219 |
|
hist_scores | 0.220 | 0.000 | 0.218 |
|
list_genes | 0.100 | 0.016 | 0.117 |
|
microarray2dataset | 0.008 | 0.000 | 0.009 |
|
pValue_GO | 0 | 0 | 0 |
|
plot_design | 0.152 | 0.000 | 0.153 |
|
prefix2dataset | 0.008 | 0.000 | 0.010 |
|
quantiles_scores | 0.208 | 0.016 | 0.224 |
|
rerank | 0.236 | 0.016 | 0.249 |
|
subEset | 0.044 | 0.004 | 0.048 |
|
subset_scores | 0.392 | 0.024 | 0.416 |
|
table_genes | 0.108 | 0.004 | 0.111 |
|