BioC 3.2: CHECK report for GOexpress on perceval

Package: GOexpress

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.3.2.tar.gz

StartedAt: 2015-08-24 01:22:20 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:25:13 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 173.0 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GOexpress.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.3.2’
* 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/15s] 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
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’
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’
microarray2dataset.build: no visible global function definition for
  ‘getCurlHandle’
prefix2dataset.build: no visible global function definition for
  ‘getCurlHandle’
sampleEnsemblGeneId: no visible global function definition for
  ‘getCurlHandle’
* 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 ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
GO_analyse          14.041  0.205  14.247
AlvMac_results.pVal 10.270  0.983  11.397
* 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
  ‘/Users/biocbuild/bbs-3.2-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	0.153	0.015	0.167
AlvMac_GOgenes	0.610	0.019	0.629
AlvMac_allGO	0.040	0.005	0.045
AlvMac_allgenes	0.015	0.001	0.016
AlvMac_results	0.482	0.030	0.512
AlvMac_results.pVal	10.270	0.983	11.397
GO_analyse	14.041	0.205	14.247
GOexpress-package	0.005	0.001	0.005
cluster_GO	0.511	0.028	0.540
expression_plot	1.108	0.053	1.162
expression_plot_symbol	1.067	0.016	1.082
expression_profiles	0.744	0.010	0.755
expression_profiles_symbol	0.906	0.012	0.918
heatmap_GO	1.131	0.021	1.152
hist_scores	0.377	0.042	0.419
list_genes	0.168	0.013	0.181
microarray2dataset	0.028	0.006	0.034
overlap_GO	1.237	0.328	1.650
pValue_GO	0.001	0.000	0.001
plot_design	0.243	0.045	0.289
prefix2dataset	0.019	0.002	0.021
quantiles_scores	0.550	0.041	0.597
rerank	0.323	0.018	0.342
subEset	0.042	0.001	0.043
subset_scores	0.283	0.013	0.296
table_genes	0.538	0.020	0.557