Multiple platform build/check report for BioC 3.9 - CHECK report for GOexpress on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GOexpress_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GOexpress.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
AlvMac_results.pVal 6.869  2.516   9.959
GO_analyse          5.052  0.338   5.659
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GOexpress.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GOexpress
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GOexpress’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOexpress)

Tests output

Example timings

name	user	system	elapsed
AlvMac	0.299	0.067	0.370
AlvMac_GOgenes	0.144	0.028	0.174
AlvMac_allGO	0.044	0.008	0.052
AlvMac_allgenes	0.027	0.004	0.031
AlvMac_results	0.257	0.036	0.303
AlvMac_results.pVal	6.869	2.516	9.959
GO_analyse	5.052	0.338	5.659
GOexpress-package	0.015	0.009	0.024
cluster_GO	0.257	0.034	0.294
expression_plot	2.051	0.058	2.233
expression_plot_symbol	1.773	0.017	1.900
expression_profiles	1.620	0.012	1.787
expression_profiles_symbol	2.111	0.047	2.293
heatmap_GO	1.512	0.047	1.684
hist_scores	0.410	0.049	0.534
list_genes	0.187	0.010	0.204
microarray2dataset	0.037	0.015	0.051
pValue_GO	0.000	0.000	0.001
plot_design	0.292	0.015	0.367
prefix2dataset	0.030	0.008	0.038
quantiles_scores	0.260	0.014	0.278
rerank	0.400	0.029	0.438
subEset	0.063	0.004	0.073
subset_scores	0.356	0.020	0.376
table_genes	0.168	0.032	0.200

CHECK report for GOexpress on celaya2

Summary

Command output

Installation output

Tests output

Example timings