scone 1.1.2
Michael Cole
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scone | | Last Changed Rev: 130908 / Revision: 131943 | | Last Changed Date: 2017-07-03 12:10:13 -0400 (Mon, 03 Jul 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf scone.buildbin-libdir scone.Rcheck && mkdir scone.buildbin-libdir scone.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=scone.buildbin-libdir scone_1.1.2.tar.gz >scone.Rcheck\00install.out 2>&1 && cp scone.Rcheck\00install.out scone-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=scone.buildbin-libdir --install="check:scone-install.out" --force-multiarch --no-vignettes --timings scone_1.1.2.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scone/DESCRIPTION' ... OK
* this is package 'scone' version '1.1.2'
* 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 'scone' 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 ... NOTE
'library' or 'require' calls in package code:
'ggplot2' 'plotly' 'visNetwork'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'shiny::renderPlotly'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sconeReport: no visible global function definition for
'visNetworkOutput'
sconeReport: no visible global function definition for 'plotlyOutput'
sconeReport : server: no visible global function definition for
'renderVisNetwork'
sconeReport : server: no visible global function definition for '%>%'
sconeReport : server: no visible global function definition for
'visNetwork'
sconeReport : server: no visible global function definition for
'visHierarchicalLayout'
sconeReport : server: no visible global function definition for
'visGroups'
sconeReport : server: no visible global function definition for
'visEdges'
sconeReport : server: no visible global function definition for
'visOptions'
sconeReport : server: no visible global function definition for
'visLegend'
sconeReport : server: no visible global function definition for
'visNetworkProxy'
sconeReport : server: no visible global function definition for
'visSelectNodes'
sconeReport : server: no visible global function definition for
'setNames'
sconeReport : server: no visible global function definition for
'plot_ly'
sconeReport : server: no visible global function definition for
'ggplot'
sconeReport : server: no visible global function definition for 'aes'
sconeReport : server: no visible global function definition for
'geom_bar'
sconeReport : server: no visible global function definition for 'ylim'
sconeReport : server: no visible global function definition for 'labs'
sconeReport : server: no visible global function definition for 'theme'
sconeReport : server: no visible global function definition for
'element_blank'
sconeReport : server: no visible global function definition for
'ggplotly'
sconeReport : server: no visible global function definition for
'geom_violin'
sconeReport : server: no visible global function definition for
'coord_cartesian'
sconeReport : server: no visible global function definition for
'scale_fill_manual'
sconeReport : server: no visible global function definition for
'geom_point'
sconeReport : server: no visible global function definition for
'guides'
sconeReport : server: no visible binding for global variable 'var'
sconeReport : server: no visible global function definition for
'boxplot'
sconeReport : server : <anonymous>: no visible global function
definition for 'write.csv'
score_matrix: no visible global function definition for 'var'
Undefined global functions or variables:
%>% aes boxplot coord_cartesian element_blank geom_bar geom_point
geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput
renderVisNetwork scale_fill_manual setNames theme var visEdges
visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput
visNetworkProxy visOptions visSelectNodes write.csv ylim
Consider adding
importFrom("graphics", "boxplot")
importFrom("stats", "setNames", "var")
importFrom("utils", "write.csv")
to your NAMESPACE file.
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/scone.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'scone' ...
** R
** data
** 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 'scone' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scone' as scone_1.1.2.zip
* DONE (scone)