metaseqR 1.10.0
Panagiotis Moulos
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/metaseqR | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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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### rm -rf metaseqR.buildbin-libdir metaseqR.Rcheck && mkdir metaseqR.buildbin-libdir metaseqR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaseqR.buildbin-libdir metaseqR_1.10.0.tar.gz >metaseqR.Rcheck\00install.out 2>&1 && cp metaseqR.Rcheck\00install.out metaseqR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=metaseqR.buildbin-libdir --install="check:metaseqR-install.out" --force-multiarch --no-vignettes --timings metaseqR_1.10.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/metaseqR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaseqR' version '1.10.0'
* 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 whether package 'metaseqR' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' '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
biasPlotToJSON: no visible binding for global variable 'nams'
cddat: no visible global function definition for 'assayData'
countsBioToJSON: no visible binding for global variable 'nams'
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 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
'readGAlignments'
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
'ScanBamParam'
read2count : <anonymous>: no visible global function definition for
'scanBamFlag'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [69s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
diagplot.de.heatmap 13.21 0.08 13.29
diagplot.volcano 7.38 0.02 7.78
diagplot.pairs 5.35 0.06 6.36
diagplot.filtered 1.35 0.04 7.28
** running examples for arch 'x64' ... [74s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
diagplot.de.heatmap 15.91 0.07 15.98
diagplot.volcano 8.48 0.05 8.53
diagplot.pairs 4.98 0.07 5.06
diagplot.filtered 1.64 0.13 7.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [44s]
[44s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [50s]
[51s] 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
'D:/biocbld/bbs-3.2-bioc/meat/metaseqR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'metaseqR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'metaseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaseqR' as metaseqR_1.10.0.zip
* DONE (metaseqR)