BioC 3.5: CHECK report for GOexpress on malbec2

Package: GOexpress

Version: 1.10.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.10.0.tar.gz

StartedAt: 2017-10-17 23:40:48 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:42:28 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 100.3 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.10.0’
* 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 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-3.5-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	0.108	0.024	0.131
AlvMac_GOgenes	0.392	0.028	0.420
AlvMac_allGO	0.020	0.004	0.023
AlvMac_allgenes	0.016	0.000	0.013
AlvMac_results	0.300	0.040	0.341
AlvMac_results.pVal	2.768	0.380	3.151
GO_analyse	2.536	0.032	2.571
GOexpress-package	0.000	0.000	0.003
cluster_GO	0.316	0.060	0.380
expression_plot	3.292	0.044	3.337
expression_plot_symbol	0.812	0.000	0.813
expression_profiles	0.600	0.004	0.602
expression_profiles_symbol	0.696	0.016	0.710
heatmap_GO	1.188	0.000	1.427
hist_scores	0.244	0.016	0.258
list_genes	0.116	0.028	0.144
microarray2dataset	0.008	0.004	0.009
pValue_GO	0.000	0.000	0.001
plot_design	0.356	0.000	0.357
prefix2dataset	0.012	0.000	0.010
quantiles_scores	0.488	0.036	0.524
rerank	0.360	0.000	0.361
subEset	0.048	0.000	0.048
subset_scores	0.180	0.052	0.230
table_genes	0.324	0.040	0.362