soGGi 1.4.4
Tom Carroll
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/soGGi | | Last Changed Rev: 117524 / Revision: 122332 | | Last Changed Date: 2016-05-15 18:53:37 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings soGGi_1.4.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/soGGi.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘soGGi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘soGGi’ version ‘1.4.4’
* 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 ‘soGGi’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘soGGi’
See ‘/home/biocbuild/bbs-3.3-bioc/meat/soGGi.Rcheck/00install.out’ for details.
* 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
Package in Depends field not imported from: ‘SummarizedExperiment’
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 ... NOTE
Foreign function call to a different package:
.Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
GetGRanges: no visible global function definition for ‘read.delim’
findconsensusRegions : <anonymous>: no visible global function
definition for ‘weighted.mean’
getShifts: no visible global function definition for
‘readGAlignmentsFromBam’
getSummitScore: no visible global function definition for
‘readGAlignmentsFromBam’
normalise.ChIPprofile: no visible global function definition for
‘assays’
normalise.ChIPprofile : <anonymous>: no visible global function
definition for ‘assays’
normalise.ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
normalise.ChIPprofile: no visible global function definition for
‘rowRanges’
normaliseQuantiles.ChIPprofile: no visible global function definition
for ‘assays’
normaliseQuantiles.ChIPprofile: no visible global function definition
for ‘SummarizedExperiment’
normaliseQuantiles.ChIPprofile: no visible global function definition
for ‘rowRanges’
plotHeatmap.ChIPprofile: no visible global function definition for
‘heat.colors’
plotHeatmap.ChIPprofile: no visible global function definition for
‘assay’
plotHeatmap.ChIPprofile: no visible global function definition for
‘layout’
plotHeatmap.ChIPprofile: no visible global function definition for
‘par’
plotRegion.ChIPprofile: no visible global function definition for
‘assays’
plotRegion.ChIPprofile : <anonymous>: no visible global function
definition for ‘rowRanges’
plotRegion.ChIPprofile: no visible global function definition for
‘rowRanges’
plotRegion.ChIPprofile: no visible global function definition for
‘rowRanges<-’
plotRegion.ChIPprofile: no visible global function definition for
‘formula’
runFindSummit: no visible global function definition for
‘readGAlignmentsFromBam’
runRegionPlot: no visible global function definition for
‘SummarizedExperiment’
runRegionPlot : <anonymous>: no visible global function definition for
‘spline’
summitPipeline: no visible global function definition for
‘readGAlignmentsFromBam’
zeroToMin2: no visible global function definition for ‘assays’
zeroToMin2: no visible global function definition for ‘assays<-’
Ops,ChIPprofile-ChIPprofile: no visible global function definition for
‘assays’
Ops,ChIPprofile-ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
Ops,ChIPprofile-ChIPprofile: no visible global function definition for
‘rowRanges’
Ops,ChIPprofile-numeric: no visible global function definition for
‘assays’
Ops,ChIPprofile-numeric: no visible global function definition for
‘SummarizedExperiment’
Ops,ChIPprofile-numeric: no visible global function definition for
‘rowRanges’
Ops,numeric-ChIPprofile: no visible global function definition for
‘assays’
Ops,numeric-ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
Ops,numeric-ChIPprofile: no visible global function definition for
‘rowRanges’
[[,ChIPprofile-ANY-missing: no visible global function definition for
‘SummarizedExperiment’
[[,ChIPprofile-ANY-missing: no visible global function definition for
‘assays’
[[,ChIPprofile-ANY-missing: no visible global function definition for
‘rowRanges’
c,ChIPprofile : <anonymous>: no visible global function definition for
‘assays’
c,ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
c,ChIPprofile: no visible global function definition for ‘rowRanges’
cbind,ChIPprofile: no visible global function definition for ‘assays’
cbind,ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
cbind,ChIPprofile: no visible global function definition for
‘rowRanges’
log2,ChIPprofile: no visible global function definition for ‘assays’
log2,ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
log2,ChIPprofile: no visible global function definition for ‘rowRanges’
log,ChIPprofile: no visible global function definition for ‘assays’
log,ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
log,ChIPprofile: no visible global function definition for ‘rowRanges’
mean,ChIPprofile: no visible global function definition for ‘assays’
mean,ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
mean,ChIPprofile: no visible global function definition for ‘rowRanges’
normalise,ChIPprofile-character-numeric: no visible global function
definition for ‘assays’
normalise,ChIPprofile-character-numeric : <anonymous>: no visible
global function definition for ‘assays’
normalise,ChIPprofile-character-numeric: no visible global function
definition for ‘SummarizedExperiment’
normalise,ChIPprofile-character-numeric: no visible global function
definition for ‘rowRanges’
normaliseQuantiles,ChIPprofile: no visible global function definition
for ‘assays’
normaliseQuantiles,ChIPprofile: no visible global function definition
for ‘SummarizedExperiment’
normaliseQuantiles,ChIPprofile: no visible global function definition
for ‘rowRanges’
plotHeatmap,ChIPprofile: no visible global function definition for
‘heat.colors’
plotHeatmap,ChIPprofile: no visible global function definition for
‘assay’
plotHeatmap,ChIPprofile: no visible global function definition for
‘layout’
plotHeatmap,ChIPprofile: no visible global function definition for
‘par’
plotRegion,ChIPprofile: no visible global function definition for
‘assays’
plotRegion,ChIPprofile : <anonymous>: no visible global function
definition for ‘rowRanges’
plotRegion,ChIPprofile: no visible global function definition for
‘rowRanges’
plotRegion,ChIPprofile: no visible global function definition for
‘rowRanges<-’
plotRegion,ChIPprofile: no visible global function definition for
‘formula’
rbind,ChIPprofile: no visible global function definition for ‘assays’
rbind,ChIPprofile : <anonymous>: no visible global function definition
for ‘rowRanges’
rbind,ChIPprofile: no visible global function definition for
‘SummarizedExperiment’
Undefined global functions or variables:
SummarizedExperiment assay assays assays<- formula heat.colors layout
par read.delim readGAlignmentsFromBam rowRanges rowRanges<- spline
weighted.mean
Consider adding
importFrom("grDevices", "heat.colors")
importFrom("graphics", "layout", "par")
importFrom("stats", "formula", "spline", "weighted.mean")
importFrom("utils", "read.delim")
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 ... WARNING
Undocumented arguments in documentation object 'Ops,ChIPprofile,ChIPprofile-method'
‘x’ ‘...’ ‘base’
Undocumented arguments in documentation object 'c,ChIPprofile-method'
‘x’ ‘...’ ‘recursive’ ‘deparse.level’ ‘i’ ‘name’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/soGGi.Rcheck/00check.log’
for details.