BioC 3.5: CHECK report for GOexpress on tokay2

Package: GOexpress

Version: 1.10.0

Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.10.0.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.10.0.tar.gz

StartedAt: 2017-10-18 00:17:17 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:20:49 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 211.9 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.10.0.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOexpress/DESCRIPTION' ... OK
* this is package 'GOexpress' version '1.10.0'
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
expression_plot 6.19   0.08    6.26
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GOexpress.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'GOexpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOexpress' as GOexpress_1.10.0.zip
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.17	0.02	0.19
AlvMac_GOgenes	0.47	0.00	0.46
AlvMac_allGO	0.03	0.03	0.07
AlvMac_allgenes	0.03	0.00	0.03
AlvMac_results	0.36	0.02	0.37
AlvMac_results.pVal	1.87	0.31	2.19
GO_analyse	2.92	0.12	3.04
GOexpress-package	0.00	0.02	0.01
cluster_GO	0.40	0.03	0.44
expression_plot	3.14	0.00	3.14
expression_plot_symbol	1.10	0.05	1.14
expression_profiles	0.65	0.01	0.67
expression_profiles_symbol	0.77	0.02	0.79
heatmap_GO	1.33	0.03	1.36
hist_scores	0.65	0.00	0.65
list_genes	0.13	0.00	0.13
microarray2dataset	0.00	0.01	0.01
pValue_GO	0	0	0
plot_design	0.14	0.05	0.19
prefix2dataset	0.00	0.03	0.03
quantiles_scores	0.22	0.02	0.24
rerank	0.27	0.05	0.31
subEset	0.05	0.00	0.05
subset_scores	0.28	0.01	0.30
table_genes	0.15	0.00	0.15

name	user	system	elapsed
AlvMac	0.15	0.00	0.16
AlvMac_GOgenes	0.61	0.01	0.62
AlvMac_allGO	0.03	0.00	0.03
AlvMac_allgenes	0.03	0.02	0.05
AlvMac_results	0.41	0.03	0.43
AlvMac_results.pVal	1.78	0.39	2.17
GO_analyse	3.75	0.17	3.93
GOexpress-package	0.00	0.02	0.01
cluster_GO	0.59	0.06	0.66
expression_plot	6.19	0.08	6.26
expression_plot_symbol	1.11	0.01	1.13
expression_profiles	0.95	0.03	0.98
expression_profiles_symbol	1.06	0.04	1.09
heatmap_GO	1.90	0.01	1.92
hist_scores	0.68	0.05	0.72
list_genes	0.12	0.00	0.13
microarray2dataset	0.02	0.00	0.01
pValue_GO	0	0	0
plot_design	0.42	0.03	0.46
prefix2dataset	0.01	0.00	0.01
quantiles_scores	0.22	0.01	0.24
rerank	0.25	0.07	0.31
subEset	0.05	0.01	0.06
subset_scores	0.26	0.02	0.28
table_genes	0.13	0.01	0.14