Package: GOexpress

Version: 1.12.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.12.0.tar.gz

StartedAt: 2018-04-11 23:58:12 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:59:52 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 100.6 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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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_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-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	0.128	0.004	0.131
AlvMac_GOgenes	0.420	0.004	0.421
AlvMac_allGO	0.024	0.000	0.023
AlvMac_allgenes	0.008	0.004	0.013
AlvMac_results	0.304	0.016	0.318
AlvMac_results.pVal	2.816	0.368	3.188
GO_analyse	2.560	0.008	2.568
GOexpress-package	0.000	0.004	0.004
cluster_GO	0.336	0.004	0.340
expression_plot	2.940	0.008	2.950
expression_plot_symbol	0.832	0.000	0.833
expression_profiles	0.612	0.004	0.616
expression_profiles_symbol	0.712	0.000	0.715
heatmap_GO	1.260	0.000	1.269
hist_scores	0.524	0.008	0.532
list_genes	0.088	0.004	0.092
microarray2dataset	0.008	0.004	0.013
pValue_GO	0.000	0.000	0.001
plot_design	0.148	0.000	0.147
prefix2dataset	0.008	0.004	0.012
quantiles_scores	0.224	0.008	0.232
rerank	0.444	0.004	0.452
subEset	0.052	0.000	0.054
subset_scores	0.260	0.012	0.270
table_genes	0.120	0.012	0.133