BioC 3.5: CHECK report for GOexpress on veracruz2

Package: GOexpress

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.10.0.tar.gz

StartedAt: 2017-10-18 04:21:52 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:23:44 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 112.9 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 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 6.261  0.749   7.211
* 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	0.139	0.014	0.156
AlvMac_GOgenes	0.377	0.012	0.396
AlvMac_allGO	0.025	0.002	0.027
AlvMac_allgenes	0.016	0.001	0.018
AlvMac_results	0.320	0.011	0.347
AlvMac_results.pVal	6.261	0.749	7.211
GO_analyse	3.115	0.119	3.361
GOexpress-package	0.004	0.002	0.006
cluster_GO	0.141	0.012	0.157
expression_plot	3.703	0.026	3.823
expression_plot_symbol	1.203	0.029	1.296
expression_profiles	0.758	0.012	0.786
expression_profiles_symbol	1.040	0.018	1.091
heatmap_GO	1.433	0.023	1.529
hist_scores	0.266	0.017	0.289
list_genes	0.122	0.010	0.143
microarray2dataset	0.017	0.004	0.021
pValue_GO	0.000	0.000	0.001
plot_design	0.160	0.010	0.173
prefix2dataset	0.014	0.002	0.016
quantiles_scores	0.246	0.011	0.264
rerank	0.251	0.008	0.264
subEset	0.054	0.001	0.057
subset_scores	0.406	0.013	0.429
table_genes	0.123	0.004	0.134