ENVISIONQuery 1.18.0
Alex Lisovich , Roger Day
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ENVISIONQuery | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ENVISIONQuery_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ENVISIONQuery.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 ‘ENVISIONQuery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENVISIONQuery’ version ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ENVISIONQuery’ can be installed ... [2s/2s] OK
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘XML’ ‘rJava’
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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘ENVISIONQuery/R/zzz.R’:
.onAttach calls:
cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n")
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in '?.onAttach'.
.onAttach : getJavaVersion: no visible global function definition for
‘.jcall’
.onAttach : jpackage: no visible binding for global variable
‘.jniInitialized’
.onAttach : jpackage: no visible global function definition for
‘.jinit’
.onAttach : jpackage: no visible global function definition for
‘.jaddClassPath’
.onAttach : jpackage: no visible global function definition for
‘.jaddLibrary’
ENVISIONQuery.chunk: no visible global function definition for
‘.jarray’
formatIdMap: no visible global function definition for ‘xmlTreeParse’
formatIdMap: no visible global function definition for ‘xmlRoot’
formatIdMap: no visible global function definition for ‘xmlChildren’
formatIntact: no visible global function definition for ‘xmlTreeParse’
formatIntact: no visible global function definition for ‘xmlRoot’
formatIntact: no visible global function definition for ‘xmlChildren’
formatPicr: no visible global function definition for ‘xmlTreeParse’
formatPicr: no visible global function definition for ‘xmlRoot’
formatPicr: no visible global function definition for ‘xmlChildren’
formatReactome: no visible global function definition for
‘xmlTreeParse’
formatReactome: no visible global function definition for ‘xmlRoot’
formatReactome: no visible global function definition for ‘xmlChildren’
getIdEntries: no visible global function definition for ‘xmlChildren’
getIdEntries : <anonymous>: no visible global function definition for
‘xmlAttrs’
getIdMatchInfo: no visible global function definition for ‘xmlChildren’
getIdMatchInfo : <anonymous>: no visible global function definition for
‘xmlAttrs’
getIdMatchInfo : <anonymous>: no visible global function definition for
‘xmlValue’
getIdMatchInfo : <anonymous>: no visible global function definition for
‘xmlChildren’
getInputIdEntries: no visible global function definition for
‘xmlChildren’
getInputIdEntries : <anonymous>: no visible global function definition
for ‘xmlAttrs’
getIntactMatchInfo: no visible global function definition for
‘xmlChildren’
getIntactMatchInfo : <anonymous>: no visible global function definition
for ‘xmlAttrs’
getIntactMatchInfo: no visible global function definition for
‘xmlAttrs’
getPicrMatchInfo: no visible global function definition for
‘xmlChildren’
getPicrMatchInfo : <anonymous>: no visible global function definition
for ‘xmlAttrs’
getPicrMatchInfo: no visible global function definition for ‘xmlAttrs’
getPositiveResultSetIDs: no visible global function definition for
‘xmlChildren’
getPositiveResultSetIDs: no visible global function definition for
‘xmlAttrs’
getPositiveResultSetIDs : <anonymous>: no visible global function
definition for ‘xmlAttrs’
getReactomeMatchInfo: no visible global function definition for
‘xmlChildren’
getReactomeMatchInfo : <anonymous>: no visible global function
definition for ‘xmlAttrs’
getReactomeMatchInfo: no visible global function definition for
‘xmlValue’
getReactomeMatchInfo: no visible global function definition for
‘xmlAttrs’
registerServices: no visible global function definition for ‘J’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/3s] 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/ENVISIONQuery.Rcheck/00check.log’
for details.