Package: GOexpress

Version: 1.17.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GOexpress_1.17.1.tar.gz

StartedAt: 2019-04-09 00:55:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:57:42 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 121.3 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GOexpress_1.17.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GOexpress.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.17.1’
* 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 ... 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-3.9-bioc/meat/GOexpress.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GOexpress
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
AlvMac	0.132	0.008	0.140
AlvMac_GOgenes	0.136	0.008	0.148
AlvMac_allGO	0.037	0.000	0.037
AlvMac_allgenes	0.021	0.000	0.021
AlvMac_results	0.213	0.020	0.233
AlvMac_results.pVal	2.675	0.455	3.180
GO_analyse	3.687	0.032	3.785
GOexpress-package	0.004	0.000	0.005
cluster_GO	0.196	0.015	0.212
expression_plot	1.481	0.001	1.483
expression_plot_symbol	1.388	0.000	1.486
expression_profiles	1.482	0.003	1.486
expression_profiles_symbol	1.303	0.009	1.311
heatmap_GO	0.798	0.003	0.806
hist_scores	0.394	0.005	0.398
list_genes	0.172	0.008	0.180
microarray2dataset	0.016	0.000	0.016
pValue_GO	0	0	0
plot_design	0.277	0.000	0.277
prefix2dataset	0.017	0.000	0.018
quantiles_scores	0.206	0.004	0.209
rerank	0.357	0.008	0.365
subEset	0.048	0.000	0.047
subset_scores	0.583	0.020	0.602
table_genes	0.195	0.008	0.202