charm 2.22.0
Peter Murakami
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/charm | | Branch: RELEASE_3_5 | | Last Commit: 5bebee9 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings charm_2.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/charm.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘charm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘charm’ version ‘2.22.0’
* 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 ‘charm’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’
A package should be listed in only one of these fields.
* 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:
‘SQN’ ‘fields’ ‘genefilter’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘oligo:::pm’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Rug: no visible global function definition for ‘Axis’
SQNff: no visible global function definition for ‘Mclust’
arrayImage: no visible global function definition for
‘discretize.image’
arrayPlot: no visible global function definition for ‘image.plot’
bgAdjustParameters: no visible global function definition for ‘approx’
cmdsplot: no visible global function definition for ‘pData’
cmdsplot: no visible global function definition for ‘ffapply’
cmdsplot: no visible global function definition for ‘rowSds’
cmdsplot: no visible global function definition for ‘dist’
cmdsplot: no visible global function definition for ‘cmdscale’
controlQC: no visible global function definition for ‘pData’
controlQC: no visible global function definition for ‘axis’
controlQC: no visible global function definition for ‘segments’
controlQC: no visible global function definition for ‘boxplot’
dmrFind: no visible global function definition for ‘ffapply’
dmrFind: no visible global function definition for ‘pt’
dmrPlot_paired: no visible global function definition for ‘matplot’
dmrPlot_paired: no visible global function definition for ‘matpoints’
dmrPlot_paired: no visible global function definition for ‘matlines’
dmrPlot_paired: no visible global function definition for ‘mtext’
dmrPlot_unpaired: no visible global function definition for ‘matplot’
dmrPlot_unpaired: no visible global function definition for ‘matlines’
dmrPlot_unpaired: no visible global function definition for ‘mtext’
dosmooth: no visible global function definition for ‘runmed’
edge.qvalue: no visible global function definition for ‘smooth.spline’
get.tt.paired: no visible global function definition for ‘rowVars’
plotDMRs: no visible global function definition for ‘matplot’
plotDMRs: no visible global function definition for ‘runmed’
plotRegions: no visible global function definition for ‘matplot’
plotRegions: no visible global function definition for ‘runmed’
plot_CpG: no visible global function definition for ‘start’
plot_CpG: no visible global function definition for ‘matchPattern’
regionMatch: no visible global function definition for ‘IRanges’
regionPlot_paired: no visible global function definition for ‘matplot’
regionPlot_paired: no visible global function definition for
‘matpoints’
regionPlot_paired: no visible global function definition for ‘matlines’
regionPlot_paired: no visible global function definition for ‘mtext’
regionPlot_unpaired: no visible global function definition for
‘matplot’
regionPlot_unpaired: no visible global function definition for
‘matlines’
regionPlot_unpaired: no visible global function definition for ‘mtext’
rowCor: no visible global function definition for ‘rowSds’
spatialAdjust: no visible global function definition for
‘discretize.image’
spatialAdjustVec: no visible global function definition for
‘image.smooth’
Undefined global functions or variables:
Axis IRanges Mclust approx axis boxplot cmdscale discretize.image
dist ffapply image.plot image.smooth matchPattern matlines matplot
matpoints mtext pData pt rowSds rowVars runmed segments smooth.spline
start
Consider adding
importFrom("graphics", "Axis", "axis", "boxplot", "matlines",
"matplot", "matpoints", "mtext", "segments")
importFrom("stats", "approx", "cmdscale", "dist", "pt", "runmed",
"smooth.spline", "start")
to your NAMESPACE file.
* 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 ... WARNING
Found the following significant warnings:
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/charm.Rcheck/00check.log’
for details.
* installing *source* package ‘charm’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (charm)