Rcade 1.14.0
Jonathan Cairns
| 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/Rcade | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 Rcade_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Rcade.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 ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcade’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
extdata 5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘graphics’ ‘plotrix’
All declared Imports should be used.
Packages in Depends field not imported from:
‘GenomicRanges’ ‘Rsamtools’ ‘baySeq’ ‘methods’
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
.onAttach: no visible global function definition for
‘packageDescription’
RcadeAnalysis: no visible global function definition for ‘values’
constructRcadeTable: no visible global function definition for
‘elementMetadata’
countReads: no visible global function definition for ‘ScanBamParam’
countReads: no visible global function definition for ‘seqlevels’
countReads: no visible global function definition for ‘scanBam’
countReads: no visible global function definition for ‘seqlevels<-’
countReads: no visible global function definition for ‘strand’
countReads: no visible global function definition for ‘end’
countReads: no visible global function definition for ‘start<-’
countReads: no visible global function definition for ‘width<-’
countReads: no visible global function definition for ‘countOverlaps’
defineBins: no visible global function definition for ‘IRanges’
defineBins: no visible global function definition for ‘GRanges’
defineBins: no visible global function definition for ‘DataFrame’
defineBins: no visible global function definition for ‘values<-’
describeGR: no visible global function definition for ‘elementMetadata’
diffCountsBaySeq: no visible global function definition for ‘width’
diffCountsBaySeq: no visible binding for global variable ‘getLibsizes’
diffCountsBaySeq: no visible global function definition for
‘libsizes<-’
diffCountsBaySeq: no visible binding for global variable ‘getPriors.NB’
diffCountsBaySeq: no visible binding for global variable
‘getLikelihoods’
getBamChrs: no visible global function definition for ‘scanBamHeader’
outputWriteFunction: no visible global function definition for ‘head’
outputWriteFunction: no visible global function definition for
‘write.csv’
plotBB,Rcade: no visible global function definition for ‘plot’
plotBBB,Rcade: no visible global function definition for ‘rainbow’
plotBBB,Rcade: no visible global function definition for ‘decorate3d’
plotMM,Rcade: no visible global function definition for ‘rainbow’
plotMM,Rcade: no visible global function definition for ‘plot’
plotMM,Rcade: no visible global function definition for ‘color.legend’
plotPCA,Rcade: no visible global function definition for ‘prcomp’
plotPCA,Rcade: no visible global function definition for ‘plot’
Undefined global functions or variables:
DataFrame GRanges IRanges ScanBamParam color.legend countOverlaps
decorate3d elementMetadata end getLibsizes getLikelihoods
getPriors.NB head libsizes<- packageDescription plot prcomp rainbow
scanBam scanBamHeader seqlevels seqlevels<- start<- strand values
values<- width width<- write.csv
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "plot")
importFrom("stats", "end", "prcomp")
importFrom("utils", "head", "packageDescription", "write.csv")
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 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
Examples with CPU or elapsed time > 5s
user system elapsed
RcadeAnalysis 5 0.028 5.029
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/Rcade.Rcheck/00check.log’
for details.