BioC 3.2: CHECK report for GOexpress on moscato1

Package: GOexpress

Version: 1.4.1

Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && D:\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 && D:\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: 2016-04-23 03:04:12 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:08:55 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 282.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GOexpress.Rcheck

Warnings: 1

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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-3.2-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  && D:\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 'D:/biocbld/bbs-3.2-bioc/meat/GOexpress.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 ... WARNING
Missing link or links in documentation object 'GOexpress-package.Rd':
  '[ggplot2]{ggplot2}'

Missing link or links in documentation object 'expression_plot.Rd':
  '[ggplot2]{ggplot2}'

Missing link or links in documentation object 'expression_plot_symbol.Rd':
  '[ggplot2]{ggplot2}'

Missing link or links in documentation object 'expression_profiles.Rd':
  '[ggplot2]{ggplot2}'

Missing link or links in documentation object 'expression_profiles_symbol.Rd':
  '[ggplot2]{ggplot2}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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' ... [27s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GO_analyse 5.47   0.06    5.56
** running examples for arch 'x64' ... [25s] 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 WARNING, 1 NOTE
See
  'D:/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	0.17	0.00	0.17
AlvMac_GOgenes	0.36	0.01	0.38
AlvMac_allGO	0.03	0.00	0.03
AlvMac_allgenes	0.01	0.00	0.01
AlvMac_results	0.32	0.02	0.33
AlvMac_results.pVal	3.20	0.36	3.55
GO_analyse	5.47	0.06	5.56
GOexpress-package	0.00	0.02	0.01
cluster_GO	0.36	0.01	0.38
expression_plot	1.35	0.00	1.34
expression_plot_symbol	1.51	0.02	1.53
expression_profiles	0.70	0.01	0.87
expression_profiles_symbol	1.12	0.00	1.12
heatmap_GO	0.97	0.02	0.99
hist_scores	0.51	0.00	0.52
list_genes	0.17	0.01	0.18
microarray2dataset	0.02	0.00	0.02
overlap_GO	1.20	0.49	4.68
pValue_GO	0	0	0
plot_design	0.47	0.00	0.47
prefix2dataset	0	0	0
quantiles_scores	0.19	0.00	0.19
rerank	0.56	0.00	0.56
subEset	0.03	0.00	0.03
subset_scores	0.22	0.03	0.25
table_genes	0.19	0.00	0.19

name	user	system	elapsed
AlvMac	0.12	0.04	0.15
AlvMac_GOgenes	0.39	0.00	0.39
AlvMac_allGO	0.03	0.00	0.03
AlvMac_allgenes	0	0	0
AlvMac_results	0.41	0.03	0.44
AlvMac_results.pVal	2.80	0.36	3.44
GO_analyse	4.79	0.15	4.95
GOexpress-package	0.02	0.00	0.01
cluster_GO	0.17	0.00	0.18
expression_plot	1.26	0.05	1.31
expression_plot_symbol	1.17	0.00	1.17
expression_profiles	1.11	0.00	1.10
expression_profiles_symbol	1	0	1
heatmap_GO	1.05	0.03	1.66
hist_scores	0.42	0.03	0.57
list_genes	0.42	0.00	0.42
microarray2dataset	0.01	0.00	0.02
overlap_GO	1.11	0.48	1.63
pValue_GO	0.02	0.00	0.02
plot_design	0.29	0.02	0.31
prefix2dataset	0.01	0.00	0.01
quantiles_scores	0.33	0.00	0.33
rerank	0.41	0.01	0.42
subEset	0.06	0.02	0.08
subset_scores	0.23	0.01	0.25
table_genes	0.18	0.00	0.17