BioC 3.3: CHECK report for GOexpress on windows2.bioconductor.org

Package: GOexpress

Version: 1.5.3

Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.5.3.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.5.3.tar.gz

StartedAt: 2015-10-27 02:53:08 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:55:28 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 140.4 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:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.5.3.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.5.3.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/GOexpress.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '1.5.3'
* 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'
Undefined global functions or variables:
  Colour Expression Factor LineType Profile X getCurlHandle
  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' ... [16s] OK
** running examples for arch 'x64' ... [16s] 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: 1 NOTE
See
  'c:/biocbld/bbs-3.3-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_1.5.3.zip
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.10	0.02	0.11
AlvMac_GOgenes	0.26	0.00	0.27
AlvMac_allGO	0.02	0.00	0.01
AlvMac_allgenes	0	0	0
AlvMac_results	0.22	0.00	0.22
AlvMac_results.pVal	1.75	0.28	2.03
GO_analyse	3.58	0.09	3.67
GOexpress-package	0.02	0.00	0.02
cluster_GO	0.11	0.02	0.12
expression_plot	0.71	0.01	0.74
expression_plot_symbol	0.82	0.00	0.81
expression_profiles	0.59	0.03	0.62
expression_profiles_symbol	0.69	0.00	0.69
heatmap_GO	0.61	0.00	0.61
hist_scores	0.49	0.00	0.48
list_genes	0.10	0.00	0.09
microarray2dataset	0.01	0.00	0.02
overlap_GO	0.83	0.49	1.32
pValue_GO	0	0	0
plot_design	0.39	0.03	0.42
prefix2dataset	0.01	0.00	0.02
quantiles_scores	0.17	0.00	0.17
rerank	0.19	0.02	0.20
subEset	0.03	0.00	0.03
subset_scores	0.17	0.00	0.18
table_genes	0.13	0.00	0.12

name	user	system	elapsed
AlvMac	0.11	0.00	0.11
AlvMac_GOgenes	0.34	0.02	0.36
AlvMac_allGO	0.03	0.00	0.03
AlvMac_allgenes	0	0	0
AlvMac_results	0.28	0.00	0.28
AlvMac_results.pVal	1.80	0.28	2.08
GO_analyse	3.81	0.05	3.86
GOexpress-package	0	0	0
cluster_GO	0.25	0.03	0.28
expression_plot	0.85	0.02	0.86
expression_plot_symbol	0.75	0.00	0.75
expression_profiles	0.58	0.00	0.58
expression_profiles_symbol	0.86	0.00	0.86
heatmap_GO	0.55	0.00	0.55
hist_scores	0.23	0.01	0.25
list_genes	0.24	0.02	0.25
microarray2dataset	0.00	0.01	0.01
overlap_GO	0.75	0.38	1.13
pValue_GO	0	0	0
plot_design	0.15	0.00	0.15
prefix2dataset	0	0	0
quantiles_scores	0.14	0.01	0.16
rerank	0.33	0.00	0.33
subEset	0.05	0.00	0.05
subset_scores	0.39	0.00	0.39
table_genes	0.11	0.00	0.11