BioC 3.2: CHECK report for GOexpress on oaxaca

Package: GOexpress

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOexpress_1.4.1.tar.gz

StartedAt: 2016-04-23 00:43:44 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:46:04 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 140.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GOexpress.Rcheck

Warnings: 1

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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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GOexpress.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.1’
* 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 ... [13s/14s] 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 ... WARNING
Missing link or links in documentation object 'GOexpress-package.Rd':
  ‘[ggplot2]{ggplot2}’

Missing link or links in documentation object 'expression_plot.Rd':
  ‘[ggplot2]{ggplot2}’

Missing link or links in documentation object 'expression_plot_symbol.Rd':
  ‘[ggplot2]{ggplot2}’

Missing link or links in documentation object 'expression_profiles.Rd':
  ‘[ggplot2]{ggplot2}’

Missing link or links in documentation object 'expression_profiles_symbol.Rd':
  ‘[ggplot2]{ggplot2}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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/28s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
AlvMac_results.pVal 6.58  0.618   7.936
* 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 WARNING, 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	0.152	0.008	0.217
AlvMac_GOgenes	0.383	0.012	0.395
AlvMac_allGO	0.036	0.003	0.039
AlvMac_allgenes	0.012	0.001	0.013
AlvMac_results	0.332	0.015	0.415
AlvMac_results.pVal	6.580	0.618	7.936
GO_analyse	4.315	0.105	4.435
GOexpress-package	0.006	0.003	0.008
cluster_GO	0.177	0.016	0.193
expression_plot	1.141	0.026	1.171
expression_plot_symbol	1.240	0.013	1.255
expression_profiles	0.833	0.013	0.848
expression_profiles_symbol	0.930	0.008	0.940
heatmap_GO	0.858	0.017	0.960
hist_scores	0.537	0.029	0.619
list_genes	0.138	0.007	0.145
microarray2dataset	0.018	0.005	0.127
overlap_GO	1.032	0.180	1.488
pValue_GO	0.000	0.000	0.001
plot_design	0.187	0.029	0.302
prefix2dataset	0.014	0.002	0.015
quantiles_scores	0.361	0.021	0.382
rerank	0.240	0.012	0.251
subEset	0.039	0.001	0.040
subset_scores	0.360	0.006	0.367
table_genes	0.192	0.014	1.295