BioC 3.2: CHECK report for GOexpress on windows1.bioconductor.org

Package: GOexpress

Version: 1.4.1

Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.4.1.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.4.1.tar.gz

StartedAt: 2015-10-27 02:18:34 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:20:58 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 143.6 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.4.1.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.4.1.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GOexpress.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.4.1'
* 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'
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' ... [16s] OK
** running examples for arch 'x64' ... [18s] 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-3.2-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_1.4.1.zip
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.08	0.03	0.11
AlvMac_GOgenes	0.28	0.00	0.28
AlvMac_allGO	0.02	0.00	0.02
AlvMac_allgenes	0.01	0.00	0.01
AlvMac_results	0.25	0.00	0.25
AlvMac_results.pVal	1.57	0.39	1.96
GO_analyse	3.32	0.18	3.50
GOexpress-package	0.00	0.01	0.01
cluster_GO	0.24	0.02	0.25
expression_plot	0.70	0.03	0.74
expression_plot_symbol	0.80	0.00	0.79
expression_profiles	0.61	0.03	0.65
expression_profiles_symbol	0.7	0.0	0.7
heatmap_GO	0.64	0.01	0.65
hist_scores	0.53	0.05	0.58
list_genes	0.11	0.02	0.12
microarray2dataset	0.00	0.01	0.01
overlap_GO	0.75	0.33	1.10
pValue_GO	0	0	0
plot_design	0.32	0.03	0.34
prefix2dataset	0	0	0
quantiles_scores	0.12	0.01	0.14
rerank	0.21	0.02	0.24
subEset	0.04	0.00	0.03
subset_scores	0.29	0.00	0.30
table_genes	0.14	0.00	0.14

name	user	system	elapsed
AlvMac	0.11	0.00	0.11
AlvMac_GOgenes	0.40	0.00	0.39
AlvMac_allGO	0.03	0.00	0.03
AlvMac_allgenes	0	0	0
AlvMac_results	0.29	0.00	0.30
AlvMac_results.pVal	1.74	0.39	2.12
GO_analyse	4.36	0.12	4.49
GOexpress-package	0	0	0
cluster_GO	0.14	0.00	0.14
expression_plot	0.82	0.02	0.83
expression_plot_symbol	0.99	0.03	1.01
expression_profiles	0.68	0.00	0.69
expression_profiles_symbol	0.66	0.02	0.67
heatmap_GO	0.58	0.03	0.61
hist_scores	0.23	0.04	0.28
list_genes	0.13	0.00	0.13
microarray2dataset	0.01	0.00	0.01
overlap_GO	0.77	0.41	1.17
pValue_GO	0	0	0
plot_design	0.15	0.02	0.18
prefix2dataset	0	0	0
quantiles_scores	0.16	0.00	0.16
rerank	0.2	0.0	0.2
subEset	0.05	0.00	0.05
subset_scores	0.34	0.00	0.34
table_genes	0.16	0.00	0.16