Heatplus 2.30.0
Alexander Ploner
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Heatplus |
| Branch: RELEASE_3_9 |
| Last Commit: 9df1904 |
| Last Changed Date: 2019-05-02 11:53:06 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Heatplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Heatplus_2.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Heatplus.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Heatplus/DESCRIPTION’ ... OK
* this is package ‘Heatplus’ version ‘2.30.0’
* 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 ‘Heatplus’ 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
* 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
Unexported object imported by a ':::' call: ‘stats:::plotNode’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
annHeatmap.ExpressionSet annHeatmap.default plot.annHeatmap
print.annHeatmap regHeatmap.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmapLayout: warning in layout(ll, width = ll.width, height =
ll.height, respect = TRUE): partial argument match of 'width' to
'widths'
heatmapLayout: warning in layout(ll, width = ll.width, height =
ll.height, respect = TRUE): partial argument match of 'height' to
'heights'
heatmap_2: warning in layout(ll, width = ll.width, height = ll.height,
respect = TRUE): partial argument match of 'width' to 'widths'
heatmap_2: warning in layout(ll, width = ll.width, height = ll.height,
respect = TRUE): partial argument match of 'height' to 'heights'
heatmap_plus: warning in layout(ll, width = ll.width, height =
ll.height, respect = TRUE): partial argument match of 'width' to
'widths'
heatmap_plus: warning in layout(ll, width = ll.width, height =
ll.height, respect = TRUE): partial argument match of 'height' to
'heights'
oldPicketplot: warning in matrix(c(1, 2), nc = 1): partial argument
match of 'nc' to 'ncol'
oldPicketplot: warning in axis(2, at = yy, label = label, las = TRUE,
font = 2, col = par("bg"), col.axis = par("fg"), tick = FALSE):
partial argument match of 'label' to 'labels'
oldPicketplot: warning in axis(2, at = yy, label = label, las = TRUE,
tick = FALSE, font = 2): partial argument match of 'label' to
'labels'
oldPicketplot: warning in axis(1, xx.grp, label = FALSE, tcl = -1.5):
partial argument match of 'label' to 'labels'
oldPicketplot: warning in axis(1, mids, label = grplabel, font = 2,
cex.axis = cc$cex.label, tick = FALSE): partial argument match of
'label' to 'labels'
picketPlot: warning in axis(labaxis, at = panels[[i]]$labcc, label =
panels[[i]]$label, las = las, tick = FALSE, font = 2, col =
par("bg"), col.axis = par("fg")): partial argument match of 'label'
to 'labels'
picketPlot: warning in axis(grpaxis, grpcoord, label = FALSE, tcl =
-1.5): partial argument match of 'label' to 'labels'
picketPlot: warning in axis(grpaxis, mids, label = grplabel, font = 2,
cex.axis = cc$cex.label, tick = FALSE): partial argument match of
'label' to 'labels'
BrewerClusterCol: no visible binding for global variable ‘category’
annHeatmap.ExpressionSet: no visible global function definition for
‘exprs’
annHeatmap.ExpressionSet: no visible global function definition for
‘pData’
annHeatmap2: no visible global function definition for ‘clustfun’
annHeatmap2: no visible global function definition for ‘distfun’
annHeatmap2: no visible binding for global variable ‘cuth’
annHeatmap2: no visible binding for global variable ‘asIs’
annHeatmap2: no visible binding for global variable ‘inclRef’
convAnnData: no visible global function definition for ‘na.exclude’
convAnnData: no visible global function definition for ‘model.matrix’
convAnnData: no visible global function definition for ‘naresid’
cutplot.dendrogram: no visible global function definition for
‘segments’
getLeaves: no visible global function definition for ‘dendrapply’
heatmapLayout: no visible global function definition for ‘layout.show’
print.annHeatmap: no visible global function definition for ‘show’
Undefined global functions or variables:
asIs category clustfun cuth dendrapply distfun exprs inclRef
layout.show model.matrix na.exclude naresid pData segments show
Consider adding
importFrom("graphics", "layout.show", "segments")
importFrom("methods", "show")
importFrom("stats", "dendrapply", "model.matrix", "na.exclude",
"naresid")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/Heatplus.Rcheck/00check.log’
for details.