pathview 1.8.0
Weijun Luo
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/pathview | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pathview_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/pathview.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 ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.8.0’
* 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 ‘pathview’ can be installed ... [9s/9s] 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘KEGGgraph’ ‘org.Hs.eg.db’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘pathview/R/zzz.R’:
.onLoad calls:
installed.packages()
packageStartupMessage(wordwrap(disclaimer, 80))
Package startup functions should not call ‘installed.packages’.
See section ‘Good practice’ in '?.onAttach'.
KEGGpathway2Graph2: no visible global function definition for
‘splitKEGGgroup’
KEGGpathway2Graph2: no visible global function definition for
‘expandKEGGPathway’
KEGGpathway2Graph2: no visible global function definition for ‘nodes’
KEGGpathway2Graph2: no visible global function definition for ‘edges’
KEGGpathway2Graph2: no visible global function definition for
‘getEntryID’
KEGGpathway2Graph2 : <anonymous>: no visible global function definition
for ‘getEntryID’
KEGGpathway2Graph2: no visible global function definition for
‘subGraphByNodeType’
col.key: no visible binding for global variable ‘node.sizes’
combineKEGGnodes: no visible global function definition for
‘getKEGGnodeData’
combineKEGGnodes: no visible global function definition for
‘getKEGGedgeData’
combineKEGGnodes: no visible binding for global variable ‘getName’
combineKEGGnodes: no visible binding for global variable ‘getType’
combineKEGGnodes: no visible binding for global variable ‘getComponent’
combineKEGGnodes: no visible global function definition for
‘combineNodes’
cpd2kegg: no visible binding for global variable ‘rn.list’
cpdidmap: no visible binding for global variable ‘cpd.accs’
cpdkegg2name: no visible binding for global variable ‘kegg.met’
cpdname2kegg: no visible binding for global variable ‘cpd.names’
eg2id: no visible global function definition for ‘biocLite’
eg2id: no visible global function definition for ‘mappedkeys’
id2eg: no visible global function definition for ‘biocLite’
id2eg: no visible global function definition for ‘revmap’
id2eg: no visible global function definition for ‘mappedkeys’
kegg.species.code: no visible binding for global variable ‘korg’
keggview.graph: no visible global function definition for ‘subGraph’
keggview.graph: no visible global function definition for ‘nodes’
keggview.graph: no visible global function definition for ‘degree’
keggview.graph: no visible global function definition for
‘subKEGGgraph’
keggview.graph: no visible global function definition for
‘subtypeDisplay’
keggview.graph: no visible binding for global variable
‘KEGGEdgeSubtype’
keggview.graph: no visible global function definition for
‘edgeRenderInfo<-’
keggview.graph: no visible global function definition for
‘nodeRenderInfo’
keggview.graph: no visible global function definition for
‘graphRenderInfo’
node.info: no visible global function definition for ‘nodes’
node.info: no visible global function definition for ‘getKEGGnodeData’
node.info: no visible binding for global variable ‘getName’
node.info: no visible binding for global variable ‘getType’
node.info: no visible binding for global variable ‘getComponent’
parseKGML2: no visible global function definition for ‘xmlTreeParse’
parseKGML2: no visible global function definition for ‘xmlRoot’
parseKGML2: no visible global function definition for ‘xmlChildren’
parseKGML2: no visible binding for global variable ‘xmlName’
parseKGML2: no visible global function definition for
‘parsePathwayInfo’
parseKGML2: no visible binding for global variable ‘parseEntry’
parseKGML2: no visible binding for global variable ‘parseRelation’
parseKGML2: no visible binding for global variable ‘getEntryID’
parseReaction2: no visible global function definition for ‘xmlAttrs’
parseReaction2: no visible global function definition for ‘xmlChildren’
pathview: no visible binding for global variable ‘bods’
pathview: no visible binding for global variable ‘rn.list’
reaction2edge: no visible global function definition for ‘nodes’
reaction2edge: no visible global function definition for ‘edges’
reaction2edge: no visible global function definition for ‘removeEdge’
reaction2edge: no visible global function definition for ‘addEdge’
sim.mol.data: no visible global function definition for ‘revmap’
sim.mol.data: no visible global function definition for ‘keys’
sim.mol.data: no visible binding for global variable ‘cpd.accs’
sim.mol.data: no visible binding for global variable ‘rn.list’
sim.mol.data: no visible binding for global variable ‘ko.ids’
subtypeDisplay.kedge : .local: no visible global function definition
for ‘getSubtype’
subtypeDisplay.kedge : .local: no visible global function definition
for ‘subtypeDisplay’
subtypeDisplay.kedge : .local: no visible binding for global variable
‘subtypeDisplay’
subtypeDisplay.kedge : .local: no visible global function definition
for ‘getType’
subtypeDisplay,KEGGEdge : .local: no visible global function definition
for ‘getSubtype’
subtypeDisplay,KEGGEdge : .local: no visible global function definition
for ‘subtypeDisplay’
subtypeDisplay,KEGGEdge : .local: no visible binding for global
variable ‘subtypeDisplay’
subtypeDisplay,KEGGEdge : .local: no visible global function definition
for ‘getType’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/32s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathview 13.243 0.068 14.782
eg2id 5.050 0.045 5.105
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [12s/12s]
[12s/13s] 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
‘/home/biocbuild/bbs-3.1-bioc/meat/pathview.Rcheck/00check.log’
for details.
* installing *source* package ‘pathview’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (pathview)