RCyjs 1.1.23
Paul Shannon
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCyjs | | Last Changed Rev: 107696 / Revision: 107696 | | Last Changed Date: 2015-08-23 15:30:37 -0700 (Sun, 23 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RCyjs_1.1.23.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RCyjs.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘1.1.23’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RCyjs’ can be installed ... [2s/2s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘RCyjs’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/RCyjs.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGraph,RCyjsClass: no visible global function definition for ‘printf’
httpAddGraph,RCyjsClass: no visible global function definition for
‘printf’
httpSetStyle,RCyjsClass: no visible global function definition for
‘printf’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘layoutSelectionInGrid’
Undocumented S4 methods:
generic 'layoutSelectionInGrid' and siglist 'RCyjsClass'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'RCyjsClass':
\S4method{setGraph}{RCyjsClass}
Code: function(obj, graph, hideEdges = FALSE)
Docs: function(obj, graph)
Argument names in code not in docs:
hideEdges
\S4method{setNodeAttributes}{RCyjsClass}
Code: function(obj, attribute, nodes, values)
Docs: function(obj, graph)
Argument names in code not in docs:
attribute nodes values
Argument names in docs not in code:
graph
Mismatches in argument names:
Position: 2 Code: attribute Docs: graph
\S4method{setEdgeAttributes}{RCyjsClass}
Code: function(obj, attribute, edges, values)
Docs: function(obj, graph)
Argument names in code not in docs:
attribute edges values
Argument names in docs not in code:
graph
Mismatches in argument names:
Position: 2 Code: attribute Docs: graph
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'RCyjsClass'
‘hideEdges’ ‘edgeType’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [6s/82s]
[6s/83s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘org.Hs.eg.db’
* 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: 4 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/RCyjs.Rcheck/00check.log’
for details.
* installing *source* package ‘RCyjs’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘jsonlite’: not turning on duplicate class definitions for this class.
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘RCyjs’
Creating a new generic function for ‘layout’ in package ‘RCyjs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘BiocGenerics’ seems equivalent to one from package ‘jsonlite’: not turning on duplicate class definitions for this class.
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘RCyjs’
* DONE (RCyjs)