metaseqR 1.8.1
Panagiotis Moulos
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/metaseqR | | Last Changed Rev: 108042 / Revision: 109384 | | Last Changed Date: 2015-09-02 00:10:01 -0700 (Wed, 02 Sep 2015) |
| 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 | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | 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 metaseqR_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/metaseqR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.1’
* 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 ... [43s/50s] OK
* checking installed package size ... OK
* 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
'library' or 'require' calls in package code:
‘BiocInstaller’ ‘BSgenome’ ‘GenomicRanges’ ‘parallel’ ‘RMySQL’
‘Rsamtools’ ‘RSQLite’ ‘rtracklayer’ ‘survcomp’ ‘TCC’ ‘VennDiagram’
‘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
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’
make.sample.list: no visible binding for global variable ‘file.type’
meta.perm: no visible global function definition for ‘mclapply’
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
‘strand<-’
read2count : <anonymous>: no visible global function definition for
‘strand’
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.edger: possible error in glmLRT(fit, contrast = co, test =
stat.args$test): unused argument (test = stat.args$test)
stat.edger: possible error in glmLRT(fit, coef = 2:ncol(fit$design),
test = stat.args$test): unused argument (test = stat.args$test)
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 ... [26s/28s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [43s/52s]
[44s/52s] 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/metaseqR.Rcheck/00check.log’
for details.
* installing *source* package ‘metaseqR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (metaseqR)