BioC 3.1: CHECK report for GOexpress on morelia

Package: GOexpress

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.2.2.tar.gz

StartedAt: 2015-10-09 02:30:44 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:33:05 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 141.3 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GOexpress.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.2.2’
* 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 ... [13s/13s] 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’
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 ... [25s/31s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
AlvMac_results.pVal 6.83  0.801   9.712
* 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-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.193	0.008	1.255
AlvMac_GOgenes	0.297	0.008	0.305
AlvMac_allGO	0.031	0.002	0.032
AlvMac_allgenes	0.010	0.000	0.011
AlvMac_results	0.230	0.011	0.727
AlvMac_results.pVal	6.830	0.801	9.712
GO_analyse	4.061	0.227	4.308
GOexpress-package	0.005	0.001	0.005
cluster_GO	0.283	0.018	0.301
expression_plot	0.865	0.039	0.913
expression_plot_symbol	0.967	0.054	1.023
expression_profiles	0.647	0.027	0.675
expression_profiles_symbol	0.793	0.013	0.806
heatmap_GO	0.687	0.066	0.755
hist_scores	0.296	0.021	0.318
list_genes	0.120	0.005	0.126
microarray2dataset	0.018	0.004	0.021
overlap_GO	0.935	0.287	1.565
pValue_GO	0.000	0.000	0.001
plot_design	0.227	0.025	0.254
prefix2dataset	0.016	0.002	0.018
quantiles_scores	0.288	0.012	0.301
rerank	0.263	0.008	0.272
subEset	0.048	0.000	0.049
subset_scores	0.238	0.007	0.246
table_genes	0.164	0.022	0.186