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BioC 3.5: CHECK report for GOexpress on malbec2

This page was generated on 2017-10-18 14:16:11 -0400 (Wed, 18 Oct 2017).

Package 571/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.10.0
Kevin Rue-Albrecht
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GOexpress
Branch: RELEASE_3_5
Last Commit: db8f857
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOexpress
Version: 1.10.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.10.0.tar.gz
StartedAt: 2017-10-17 23:40:48 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:42:28 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 100.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.10.0’
* 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-3.5-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:

nameusersystemelapsed
AlvMac0.1080.0240.131
AlvMac_GOgenes0.3920.0280.420
AlvMac_allGO0.0200.0040.023
AlvMac_allgenes0.0160.0000.013
AlvMac_results0.3000.0400.341
AlvMac_results.pVal2.7680.3803.151
GO_analyse2.5360.0322.571
GOexpress-package0.0000.0000.003
cluster_GO0.3160.0600.380
expression_plot3.2920.0443.337
expression_plot_symbol0.8120.0000.813
expression_profiles0.6000.0040.602
expression_profiles_symbol0.6960.0160.710
heatmap_GO1.1880.0001.427
hist_scores0.2440.0160.258
list_genes0.1160.0280.144
microarray2dataset0.0080.0040.009
pValue_GO0.0000.0000.001
plot_design0.3560.0000.357
prefix2dataset0.0120.0000.010
quantiles_scores0.4880.0360.524
rerank0.3600.0000.361
subEset0.0480.0000.048
subset_scores0.1800.0520.230
table_genes0.3240.0400.362