BioC 3.0: CHECK report for GOexpress on oaxaca

Package: GOexpress

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GOexpress_1.0.1.tar.gz

StartedAt: 2015-04-10 00:08:08 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:13:39 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 331.0 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 --no-multiarch GOexpress_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GOexpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.0.1’
* 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 ... [15s/16s] 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’
expression_plot: no visible binding for global variable ‘X’
expression_plot: no visible binding for global variable ‘Expression’
expression_plot: no visible binding for global variable ‘Factor’
expression_profiles: no visible binding for global variable ‘X’
expression_profiles: no visible binding for global variable
  ‘Expression’
expression_profiles: no visible binding for global variable ‘Profile’
expression_profiles: no visible binding for global variable ‘LineType’
expression_profiles: no visible binding for global variable ‘Colour’
mart_from_ensembl: no visible binding for global variable
  ‘prefix2dataset’
microarray_from_probeset: no visible binding for global variable
  ‘microarray2dataset’
* 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 ... [27s/156s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GO_analyse 10.165  0.157 138.675
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.309	0.008	0.374
AlvMac_results	0.611	0.015	0.626
GO_analyse	10.165	0.157	138.675
GOexpress-package	0.006	0.002	0.009
cluster_GO	0.350	0.016	0.368
expression_plot	1.263	0.022	1.288
expression_plot_symbol	1.152	0.007	1.164
expression_profiles	1.047	0.014	1.063
expression_profiles_symbol	1.063	0.008	1.075
heatmap_GO	0.806	0.014	0.866
hist_scores	0.256	0.006	0.266
list_genes	0.163	0.012	0.176
microarray2dataset	0.016	0.003	0.019
overlap_GO	1.224	0.199	2.220
plot_design	0.244	0.027	0.357
prefix2dataset	0.011	0.001	0.012
quantiles_scores	0.249	0.016	0.265
rerank	0.156	0.011	0.167
subEset	0.238	0.007	0.245
subset_scores	0.295	0.007	0.304
table_genes	0.176	0.004	0.182