BioC 3.1: CHECK report for GOexpress on moscato2

Package: GOexpress

Version: 1.2.2

Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.2.2.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.2.2.tar.gz

StartedAt: 2015-10-09 02:23:51 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:27:30 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 218.8 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.2.2.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.2.2.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/GOexpress.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.2.2'
* 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'
microarray2dataset.build: no visible global function definition for
  'getCurlHandle'
prefix2dataset.build: no visible global function definition for
  'getCurlHandle'
sampleEnsemblGeneId: no visible global function definition for
  'getCurlHandle'
* 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' ... [21s] OK
** running examples for arch 'x64' ... [22s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GO_analyse 5.15   0.11    5.26
* 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
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'GOexpress' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'GOexpress' as GOexpress_1.2.2.zip
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.10	0.04	0.15
AlvMac_GOgenes	0.33	0.00	0.32
AlvMac_allGO	0.03	0.00	0.03
AlvMac_allgenes	0	0	0
AlvMac_results	0.25	0.04	0.30
AlvMac_results.pVal	2.12	0.28	2.40
GO_analyse	4.28	0.08	4.36
GOexpress-package	0.01	0.00	0.01
cluster_GO	0.33	0.00	0.33
expression_plot	0.91	0.03	0.95
expression_plot_symbol	1.03	0.02	1.05
expression_profiles	0.60	0.01	0.62
expression_profiles_symbol	0.74	0.02	0.75
heatmap_GO	0.75	0.00	0.75
hist_scores	0.57	0.00	0.57
list_genes	0.14	0.01	0.16
microarray2dataset	0.02	0.00	0.02
overlap_GO	1.47	0.60	2.63
pValue_GO	0	0	0
plot_design	0.23	0.03	0.27
prefix2dataset	0.02	0.00	0.01
quantiles_scores	0.31	0.01	0.33
rerank	0.42	0.02	0.44
subEset	0.03	0.00	0.03
subset_scores	0.22	0.02	0.23
table_genes	0.17	0.01	0.19

name	user	system	elapsed
AlvMac	0.23	0.03	0.27
AlvMac_GOgenes	0.42	0.01	0.43
AlvMac_allGO	0.03	0.00	0.04
AlvMac_allgenes	0	0	0
AlvMac_results	0.31	0.00	0.31
AlvMac_results.pVal	2.71	0.21	2.92
GO_analyse	5.15	0.11	5.26
GOexpress-package	0.02	0.00	0.01
cluster_GO	0.37	0.01	0.39
expression_plot	1.08	0.02	1.10
expression_plot_symbol	1.23	0.00	1.23
expression_profiles	0.75	0.00	0.75
expression_profiles_symbol	0.98	0.02	1.00
heatmap_GO	0.95	0.03	0.98
hist_scores	0.29	0.01	0.30
list_genes	0.14	0.00	0.14
microarray2dataset	0.02	0.00	0.01
overlap_GO	1.12	0.43	1.58
pValue_GO	0	0	0
plot_design	0.50	0.01	0.51
prefix2dataset	0	0	0
quantiles_scores	0.17	0.00	0.17
rerank	0.25	0.02	0.27
subEset	0.03	0.00	0.03
subset_scores	0.20	0.03	0.23
table_genes	0.16	0.01	0.18