interactiveDisplay 1.7.2
Shawn Balcome
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/interactiveDisplay | | Last Changed Rev: 105062 / Revision: 107696 | | Last Changed Date: 2015-06-16 22:42:08 -0700 (Tue, 16 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | 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 interactiveDisplay_1.7.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/interactiveDisplay.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 ‘interactiveDisplay/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘interactiveDisplay’ version ‘1.7.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rstudio’
* 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 ‘interactiveDisplay’ can be installed ... [12s/12s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.altgr : <anonymous>: no visible global function definition for
‘elementMetadata’
.altgr : <anonymous>: no visible global function definition for
‘seqlevels<-’
.bicgo : <anonymous>: no visible binding for global variable ‘GO.db’
.bicgo : <anonymous>: no visible global function definition for ‘exprs’
.bicgo : <anonymous>: no visible global function definition for ‘cim’
.choose_gen: no visible global function definition for ‘ucscGenomes’
ggheat: no visible binding for global variable ‘Var2’
ggheat: no visible binding for global variable ‘Var1’
ggheat: no visible binding for global variable ‘value’
ggheat: no visible global function definition for ‘coord_flip’
subgr: no visible global function definition for ‘seqnames’
subgr: no visible global function definition for ‘seqlevels<-’
subgr: no visible global function definition for ‘ranges’
subgr2: no visible global function definition for ‘seqnames’
subgr2: no visible global function definition for ‘seqlevels<-’
subgr2: no visible global function definition for ‘ranges’
display,ExpressionSet : .local : <anonymous>: no visible global
function definition for ‘exprs’
display,ExpressionSet : .local : <anonymous>: no visible global
function definition for ‘experimentData’
display,ExpressionSet : .local : <anonymous>: no visible binding for
global variable ‘GO.db’
display,GRanges : .local: no visible global function definition for
‘mcols’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘AnnotationTrack’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘GenomeAxisTrack’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘IdeogramTrack’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘plotTracks’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘layout_circle’
display,GRanges : .local : <anonymous>: no visible binding for global
variable ‘seqnames’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘seqnames’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘ranges’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘ucscGenomes’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘GRanges’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘IRanges’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘seqlengths<-’
display,GRanges : .local : <anonymous>: no visible global function
definition for ‘seqlengths’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘mcols’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘AnnotationTrack’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘GenomeAxisTrack’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘IdeogramTrack’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘plotTracks’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘layout_circle’
display,GRangesList : .local : <anonymous>: no visible binding for
global variable ‘seqnames’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘seqnames’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘ranges’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘ucscGenomes’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘GRanges’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘IRanges’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘seqlengths<-’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘seqlengths’
display,GRangesList : .local : <anonymous>: no visible global function
definition for ‘GRangesList’
display,MRexperiment : <anonymous>: no visible global function
definition for ‘MRcounts’
display,MRexperiment : <anonymous>: no visible global function
definition for ‘pData’
display,MRexperiment : <anonymous>: no visible global function
definition for ‘plotFeature’
display,MRexperiment : <anonymous>: no visible global function
definition for ‘plotOrd’
display,MRexperiment : <anonymous>: no visible global function
definition for ‘libSize’
display,MRexperiment : <anonymous>: no visible global function
definition for ‘fData’
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for ‘seqnames’
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for ‘rowRanges’
display,RangedSummarizedExperiment : <anonymous>: no visible global
function definition for ‘assays’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
for global variable ‘Var1’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
for global variable ‘Var2’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
for global variable ‘value’
* 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 ... [7s/7s] 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-3.2-bioc/meat/interactiveDisplay.Rcheck/00check.log’
for details.
* installing *source* package ‘interactiveDisplay’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Bioconductor version 3.2 (BiocInstaller 1.19.13), ?biocLite for help
in method for ‘display’ with signature ‘object="GRanges"’: no definition for class “GRanges”
in method for ‘display’ with signature ‘object="GRangesList"’: no definition for class “GRangesList”
in method for ‘display’ with signature ‘object="RangedSummarizedExperiment"’: no definition for class “RangedSummarizedExperiment”
in method for ‘display’ with signature ‘object="MRexperiment"’: no definition for class “MRexperiment”
** 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 ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (interactiveDisplay)