BioC 3.4: CHECK report for GOexpress on malbec1

Package: GOexpress

Version: 1.8.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.8.1.tar.gz

StartedAt: 2017-04-14 22:56:42 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:58:17 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 94.7 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GOexpress.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.1’
* 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 ... 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-3.4-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	0.208	0.008	0.214
AlvMac_GOgenes	0.364	0.000	0.364
AlvMac_allGO	0.028	0.000	0.026
AlvMac_allgenes	0.008	0.000	0.007
AlvMac_results	0.260	0.004	0.266
AlvMac_results.pVal	2.676	0.316	2.992
GO_analyse	3.132	0.012	3.146
GOexpress-package	0.004	0.000	0.003
cluster_GO	0.296	0.016	0.314
expression_plot	0.856	0.024	0.879
expression_plot_symbol	0.968	0.000	0.968
expression_profiles	0.628	0.000	0.630
expression_profiles_symbol	0.696	0.004	0.698
heatmap_GO	0.572	0.012	0.583
hist_scores	0.424	0.024	0.448
list_genes	0.084	0.004	0.086
microarray2dataset	0.016	0.004	0.018
overlap_GO	1.044	0.084	1.132
pValue_GO	0	0	0
plot_design	0.136	0.000	0.138
prefix2dataset	0.004	0.004	0.007
quantiles_scores	0.324	0.000	0.324
rerank	0.196	0.000	0.196
subEset	0.032	0.000	0.033
subset_scores	0.356	0.000	0.353
table_genes	0.096	0.004	0.103