BioC 3.0: CHECK report for GOexpress on moscato1

Package: GOexpress

Version: 1.0.1

Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.0.1.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.0.1.tar.gz

StartedAt: 2015-04-10 01:46:10 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:52:15 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 365.5 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.0.1.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.0.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GOexpress.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOexpress/DESCRIPTION' ... OK
* this is package 'GOexpress' version '1.0.1'
* 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 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'
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'
microarray_from_probeset: no visible binding for global variable
  'microarray2dataset'
* 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' ... [86s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GO_analyse 8.56   0.22   65.28
** running examples for arch 'x64' ... [83s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GO_analyse 8.82   0.25   64.62
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-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_1.0.1.zip
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.23	0.00	0.23
AlvMac_results	0.47	0.01	0.49
GO_analyse	8.56	0.22	65.28
GOexpress-package	0.02	0.00	0.02
cluster_GO	0.5	0.0	0.5
expression_plot	1.20	0.02	1.21
expression_plot_symbol	1.42	0.00	1.42
expression_profiles	0.80	0.01	0.81
expression_profiles_symbol	1.03	0.00	2.50
heatmap_GO	1.22	0.00	1.21
hist_scores	0.36	0.00	0.36
list_genes	0.51	0.00	0.51
microarray2dataset	0.02	0.00	0.02
overlap_GO	1.83	0.64	2.51
plot_design	0.31	0.03	0.34
prefix2dataset	0.01	0.00	0.02
quantiles_scores	0.53	0.00	0.53
rerank	0.21	0.00	0.20
subEset	0.06	0.02	0.08
subset_scores	0.56	0.00	0.56
table_genes	0.22	0.00	0.22

name	user	system	elapsed
AlvMac	0.30	0.00	0.75
AlvMac_results	0.62	0.00	0.62
GO_analyse	8.82	0.25	64.62
GOexpress-package	0	0	0
cluster_GO	0.38	0.00	0.38
expression_plot	1.24	0.00	1.24
expression_plot_symbol	1.39	0.00	1.38
expression_profiles	1.35	0.02	1.38
expression_profiles_symbol	1.03	0.00	1.03
heatmap_GO	0.88	0.03	0.90
hist_scores	0.25	0.00	0.25
list_genes	0.17	0.00	0.17
microarray2dataset	0.01	0.00	0.02
overlap_GO	1.78	0.47	2.28
plot_design	0.53	0.00	0.53
prefix2dataset	0.02	0.00	0.01
quantiles_scores	0.29	0.01	0.31
rerank	0.19	0.00	0.19
subEset	0.07	0.00	0.07
subset_scores	0.38	0.04	0.41
table_genes	0.48	0.01	0.50

BioC 3.0: CHECK report for GOexpress on moscato1

Summary

Command output