BioC 3.0: CHECK report for GOexpress on zin1

Package: GOexpress

Version: 1.0.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.0.1.tar.gz

StartedAt: 2015-04-10 00:36:07 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:41:04 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 296.8 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/GOexpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.0.1’
* 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 ... [12s/12s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/170s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GO_analyse 6.88  0.032 153.989
* 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
  ‘/home/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	0.264	0.000	0.282
AlvMac_results	0.536	0.004	0.619
GO_analyse	6.880	0.032	153.989
GOexpress-package	0.004	0.000	0.005
cluster_GO	0.348	0.004	0.385
expression_plot	1.096	0.008	1.109
expression_plot_symbol	1.200	0.000	1.262
expression_profiles	0.861	0.008	0.904
expression_profiles_symbol	0.916	0.004	1.028
heatmap_GO	0.700	0.016	0.782
hist_scores	0.204	0.004	0.211
list_genes	0.140	0.000	0.138
microarray2dataset	0.012	0.000	0.011
overlap_GO	1.396	0.044	1.981
plot_design	0.412	0.000	0.758
prefix2dataset	0.008	0.000	0.014
quantiles_scores	0.192	0.000	0.192
rerank	0.116	0.000	0.115
subEset	0.048	0.000	0.047
subset_scores	0.248	0.000	0.256
table_genes	0.320	0.000	0.319