Package: GOexpress

Version: 1.14.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GOexpress_1.14.0.tar.gz

StartedAt: 2018-10-16 00:53:27 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:54:49 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 82.1 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GOexpress_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GOexpress.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.14.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/GOexpress.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GOexpress
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘GOexpress’ ...
** 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
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.104	0.000	0.103
AlvMac_GOgenes	0.088	0.004	0.092
AlvMac_allGO	0.024	0.000	0.025
AlvMac_allgenes	0.028	0.000	0.028
AlvMac_results	0.144	0.008	0.154
AlvMac_results.pVal	2.616	0.432	3.049
GO_analyse	2.624	0.024	2.648
GOexpress-package	0.004	0.000	0.004
cluster_GO	0.196	0.004	0.201
expression_plot	1.208	0.000	1.211
expression_plot_symbol	0.984	0.000	0.987
expression_profiles	0.872	0.000	0.874
expression_profiles_symbol	1.068	0.000	1.070
heatmap_GO	0.500	0.004	0.502
hist_scores	0.584	0.004	0.587
list_genes	0.096	0.004	0.100
microarray2dataset	0.004	0.008	0.010
pValue_GO	0.000	0.000	0.001
plot_design	0.152	0.000	0.152
prefix2dataset	0.008	0.000	0.011
quantiles_scores	0.148	0.004	0.154
rerank	0.216	0.008	0.221
subEset	0.040	0.000	0.042
subset_scores	0.180	0.004	0.184
table_genes	0.368	0.004	0.373