metaseqR 1.4.13
Panagiotis Moulos
| 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/metaseqR | | Last Changed Rev: 98198 / Revision: 102249 | | Last Changed Date: 2015-01-09 07:29:20 -0800 (Fri, 09 Jan 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metaseqR_1.4.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/metaseqR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR’ version ‘1.4.13’
* package encoding: UTF-8
* 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 ‘metaseqR’ can be installed ... [37s/38s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘BSgenome’ ‘BiocInstaller’ ‘GenomicRanges’ ‘MADAM’ ‘RMySQL’ ‘RSQLite’
‘Rsamtools’ ‘TCC’ ‘VennDiagram’ ‘parallel’ ‘rtracklayer’ ‘survcomp’
‘zoo’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘metaseqR/R/zzz.R’:
.onLoad calls:
packageStartupMessage("\n\nWelcome to metaseqR 1.4.12. Please do not ", "include \"bayseq\" in the statistics\nargument in metaseqr calls. ", "There is an incompatibility with the latest\nversion of baySeq which ", "we are fixing right now...\n\n")
See section ‘Good practice’ in '?.onAttach'.
cddat: no visible global function definition for ‘assayData’
diagplot.edaseq: no visible global function definition for
‘AnnotatedDataFrame’
diagplot.venn: no visible global function definition for
‘draw.pairwise.venn’
diagplot.venn: no visible global function definition for
‘draw.triple.venn’
diagplot.venn: no visible global function definition for
‘draw.quad.venn’
diagplot.venn: no visible global function definition for
‘draw.quintuple.venn’
estimate.aufc.weights : <anonymous>: no visible global function
definition for ‘rollmean’
get.gc.content: no visible global function definition for ‘GRanges’
get.gc.content: no visible global function definition for ‘Rle’
get.gc.content: no visible global function definition for ‘IRanges’
get.gc.content: no visible global function definition for
‘makeGRangesFromDataFrame’
get.gc.content: no visible global function definition for ‘getSeq’
get.gc.content: no visible global function definition for
‘alphabetFrequency’
get.ucsc.annotation: no visible global function definition for
‘dbDriver’
get.ucsc.annotation: no visible global function definition for
‘dbConnect’
get.ucsc.annotation: no visible global function definition for
‘dbGetQuery’
get.ucsc.annotation: no visible global function definition for
‘dbDisconnect’
get.ucsc.annotation : <anonymous>: no visible global function
definition for ‘makeGRangesFromDataFrame’
get.ucsc.annotation: no visible global function definition for
‘seqnames’
get.ucsc.annotation: no visible global function definition for ‘strand’
get.ucsc.dbl: no visible global function definition for ‘dbDriver’
get.ucsc.dbl: no visible global function definition for ‘dbConnect’
get.ucsc.dbl: no visible global function definition for ‘dbWriteTable’
get.ucsc.dbl: no visible global function definition for ‘dbDisconnect’
load.bs.genome: no visible global function definition for
‘installed.genomes’
load.bs.genome: no visible global function definition for ‘getBSgenome’
load.bs.genome: no visible global function definition for ‘biocLite’
meta.perm: no visible global function definition for ‘mclapply’
meta.test : <anonymous>: no visible global function definition for
‘fisher.method’
meta.test : <anonymous>: no visible global function definition for
‘fisher.method.perm’
meta.test : <anonymous>: no visible binding for global variable
‘combine.test’
normalize.edaseq: no visible global function definition for
‘AnnotatedDataFrame’
normalize.noiseq: no visible global function definition for ‘assayData’
read2count: no visible global function definition for ‘GRanges’
read2count: no visible global function definition for ‘Rle’
read2count: no visible global function definition for ‘IRanges’
read2count: no visible global function definition for
‘makeGRangesFromDataFrame’
read2count: no visible global function definition for ‘seqnames’
read2count: no visible global function definition for ‘strand’
read2count : <anonymous>: no visible global function definition for
‘import.bed’
read2count : <anonymous>: no visible global function definition for
‘seqnames’
read2count : <anonymous>: no visible global function definition for
‘seqlevels’
read2count : <anonymous>: no visible global function definition for
‘countOverlaps’
read2count: no visible global function definition for ‘asBam’
read2count : <anonymous>: no visible global function definition for
‘BamFile’
read2count : <anonymous>: no visible global function definition for
‘countBam’
read2count : <anonymous>: no visible global function definition for
‘summarizeOverlaps’
read2count : <anonymous>: no visible global function definition for
‘assays’
reduce.exons : <anonymous>: no visible global function definition for
‘reduce’
reduce.exons : <anonymous>: no visible global function definition for
‘DataFrame’
reduce.exons : <anonymous>: no visible global function definition for
‘mcols<-’
stat.deseq: no visible global function definition for ‘sizeFactors<-’
stat.nbpseq: no visible global function definition for ‘sizeFactors<-’
stat.noiseq: no visible global function definition for ‘assayData’
stat.noiseq: no visible global function definition for ‘sizeFactors<-’
wapply: no visible global function definition for ‘mclapply’
* 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 ... [23s/23s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [29s/40s]
[30s/41s] 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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/metaseqR.Rcheck/00check.log’
for details.