BioC 3.5: CHECK report for GOexpress on toluca2

Package: GOexpress

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.9.2.tar.gz

StartedAt: 2017-04-23 04:44:49 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:47:07 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 137.7 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.9.2’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
AlvMac_results.pVal 7.723  0.756   8.627
expression_plot     5.196  0.051   5.313
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
AlvMac	0.204	0.013	0.221
AlvMac_GOgenes	0.409	0.011	0.423
AlvMac_allGO	0.032	0.002	0.034
AlvMac_allgenes	0.022	0.001	0.023
AlvMac_results	0.333	0.012	0.346
AlvMac_results.pVal	7.723	0.756	8.627
GO_analyse	3.629	0.096	3.813
GOexpress-package	0.005	0.003	0.007
cluster_GO	0.211	0.015	0.234
expression_plot	5.196	0.051	5.313
expression_plot_symbol	1.271	0.007	1.312
expression_profiles	0.919	0.004	0.940
expression_profiles_symbol	1.051	0.004	1.078
heatmap_GO	1.858	0.014	1.900
hist_scores	0.335	0.014	0.354
list_genes	0.144	0.008	0.152
microarray2dataset	0.023	0.004	0.030
pValue_GO	0.001	0.000	0.001
plot_design	0.195	0.006	0.204
prefix2dataset	0.019	0.002	0.021
quantiles_scores	0.501	0.006	0.510
rerank	0.261	0.006	0.271
subEset	0.079	0.001	0.081
subset_scores	0.280	0.008	0.289
table_genes	0.144	0.003	0.151