marray 1.44.0
Yee Hwa (Jean) Yang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/marray | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 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-3.0-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/marray.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.44.0’
* 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 ‘marray’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
installed size is 8.0Mb
sub-directories of 1Mb or more:
doc 1.6Mb
swirldata 5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
'library' or 'require' call to ‘tkWidgets’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘limma’
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
maImage: warning in layout(matrix(c(1, 2), 1, 2), width = c(8, 2)):
partial argument match of 'width' to 'widths'
widget.marrayInfo : inputInfo: warning in assign(newname, newInfo, env
= .GlobalEnv): partial argument match of 'env' to 'envir'
widget.marrayLayout : inputLayout: warning in assign(newname,
newLayout, env = .GlobalEnv): partial argument match of 'env' to
'envir'
widget.marrayRaw : inputRaw: warning in assign(newname, newRaw, env =
.GlobalEnv): partial argument match of 'env' to 'envir'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
findID: no visible binding for global variable ‘gnames’
findID: no visible global function definition for ‘phenoData’
htmlPage: no visible binding for global variable ‘Gnames’
maTwoSamples: no visible global function definition for ‘gpTools’
scale.na: no visible global function definition for ‘applyy’
widget.TwoSamples: no visible binding for global variable ‘fileBrowser’
widget.TwoSamples: no visible global function definition for
‘widgetRender’
widget.TwoSamples: no visible global function definition for
‘values.Widget’
widget.mapGeneInfo: no visible global function definition for
‘widgetRender’
widget.mapGeneInfo: no visible global function definition for
‘values.Widget’
widget.marrayInfo : inputInfo: no visible global function definition
for ‘tclvalue’
widget.marrayInfo : fileBrow: no visible global function definition for
‘tkdelete’
widget.marrayInfo : fileBrow: no visible global function definition for
‘fileBrowser’
widget.marrayInfo : fileBrow: no visible global function definition for
‘tkinsert’
widget.marrayInfo: no visible global function definition for
‘tktoplevel’
widget.marrayInfo: no visible global function definition for
‘tkwm.title’
widget.marrayInfo: no visible global function definition for ‘tkframe’
widget.marrayInfo: no visible global function definition for ‘tkpack’
widget.marrayInfo: no visible global function definition for ‘tklabel’
widget.marrayInfo: no visible global function definition for ‘tkentry’
widget.marrayInfo: no visible global function definition for ‘tkbutton’
widget.marrayInfo: no visible global function definition for ‘tkgrid’
widget.marrayInfo: no visible global function definition for
‘tkgrid.configure’
widget.marrayInfo : <anonymous>: no visible global function definition
for ‘tkdestroy’
widget.marrayLayout : inputLayout: no visible global function
definition for ‘tclvalue’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tktoplevel’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tkwm.title’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tkframe’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tkpack’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tklabel’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tkcheckbutton’
widget.marrayLayout : listColnames : getResults: no visible global
function definition for ‘tclvalue’
widget.marrayLayout : listColnames : getResults: no visible global
function definition for ‘tkdestroy’
widget.marrayLayout : listColnames: no visible global function
definition for ‘tkbutton’
widget.marrayLayout : fileBrow: no visible global function definition
for ‘tkdelete’
widget.marrayLayout : fileBrow: no visible global function definition
for ‘fileBrowser’
widget.marrayLayout : fileBrow: no visible global function definition
for ‘tkinsert’
widget.marrayLayout: no visible global function definition for
‘tktoplevel’
widget.marrayLayout: no visible global function definition for
‘tkwm.title’
widget.marrayLayout: no visible global function definition for
‘tkframe’
widget.marrayLayout: no visible global function definition for ‘tkpack’
widget.marrayLayout: no visible global function definition for
‘tklabel’
widget.marrayLayout: no visible global function definition for
‘tkentry’
widget.marrayLayout: no visible global function definition for ‘tkgrid’
widget.marrayLayout: no visible global function definition for
‘tkgrid.configure’
widget.marrayLayout: no visible global function definition for
‘tkconfigure’
widget.marrayLayout: no visible global function definition for
‘tkbutton’
widget.marrayLayout : <anonymous>: no visible global function
definition for ‘tclvalue’
widget.marrayLayout : <anonymous>: no visible global function
definition for ‘tkdestroy’
widget.marrayRaw : inputRaw: no visible global function definition for
‘tclvalue’
widget.marrayRaw : filesClick: no visible global function definition
for ‘fileBrowser’
widget.marrayRaw : browserToEntry: no visible global function
definition for ‘objectBrowser’
widget.marrayRaw : browserToEntry: no visible global function
definition for ‘tkdelete’
widget.marrayRaw : browserToEntry: no visible global function
definition for ‘tkinsert’
widget.marrayRaw: no visible global function definition for
‘tktoplevel’
widget.marrayRaw: no visible global function definition for
‘tkwm.title’
widget.marrayRaw: no visible global function definition for ‘tkframe’
widget.marrayRaw: no visible global function definition for ‘tkpack’
widget.marrayRaw: no visible global function definition for ‘tkbutton’
widget.marrayRaw: no visible global function definition for ‘tklabel’
widget.marrayRaw: no visible global function definition for ‘tkentry’
widget.marrayRaw: no visible global function definition for ‘tkgrid’
widget.marrayRaw: no visible global function definition for
‘tkgrid.configure’
widget.marrayRaw : <anonymous>: no visible global function definition
for ‘tkdestroy’
show,ShowLargeObject: no visible global function definition for
‘printHead’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
maNormMain 12.689 0.004 12.724
* 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
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/marray.Rcheck/00check.log’
for details.