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BioC 3.5: CHECK report for metaseqR on tokay2

This page was generated on 2017-08-16 13:23:04 -0400 (Wed, 16 Aug 2017).

Package 796/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR 1.16.0
Panagiotis Moulos
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/metaseqR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metaseqR
Version: 1.16.0
Command: rm -rf metaseqR.buildbin-libdir metaseqR.Rcheck && mkdir metaseqR.buildbin-libdir metaseqR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaseqR.buildbin-libdir metaseqR_1.16.0.tar.gz >metaseqR.Rcheck\00install.out 2>&1 && cp metaseqR.Rcheck\00install.out metaseqR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=metaseqR.buildbin-libdir --install="check:metaseqR-install.out" --force-multiarch --no-vignettes --timings metaseqR_1.16.0.tar.gz
StartedAt: 2017-08-16 01:06:53 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:16:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 552.5 seconds
RetCode: 0
Status:  OK  
CheckDir: metaseqR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf metaseqR.buildbin-libdir metaseqR.Rcheck && mkdir metaseqR.buildbin-libdir metaseqR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaseqR.buildbin-libdir metaseqR_1.16.0.tar.gz >metaseqR.Rcheck\00install.out 2>&1 && cp metaseqR.Rcheck\00install.out metaseqR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=metaseqR.buildbin-libdir --install="check:metaseqR-install.out" --force-multiarch --no-vignettes --timings metaseqR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/metaseqR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.16.0'
* 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'
cddat: no visible global function definition for 'ks.test'
cddat: no visible global function definition for 'p.adjust'
cdplot: no visible global function definition for 'plot'
cdplot: no visible global function definition for 'lines'
countsBioToJSON: no visible binding for global variable 'nams'
diagplot.avg.ftd : <anonymous>: no visible binding for global variable
  'sd'
diagplot.avg.ftd: no visible global function definition for 'par'
diagplot.avg.ftd: no visible global function definition for 'plot.new'
diagplot.avg.ftd: no visible global function definition for
  'plot.window'
diagplot.avg.ftd: no visible global function definition for 'axis'
diagplot.avg.ftd: no visible global function definition for 'lines'
diagplot.avg.ftd: no visible global function definition for 'grid'
diagplot.avg.ftd: no visible global function definition for 'title'
diagplot.cor: no visible global function definition for 'cor'
diagplot.cor: no visible global function definition for
  'colorRampPalette'
diagplot.edaseq: no visible global function definition for
  'AnnotatedDataFrame'
diagplot.edaseq: no visible global function definition for 'grid'
diagplot.filtered: no visible global function definition for 'par'
diagplot.filtered: no visible global function definition for 'plot.new'
diagplot.filtered: no visible global function definition for
  'plot.window'
diagplot.filtered: no visible global function definition for 'axis'
diagplot.filtered: no visible global function definition for 'text'
diagplot.filtered: no visible global function definition for 'title'
diagplot.filtered: no visible global function definition for 'mtext'
diagplot.filtered: no visible global function definition for 'grid'
diagplot.ftd: no visible global function definition for 'par'
diagplot.ftd: no visible global function definition for 'plot.new'
diagplot.ftd: no visible global function definition for 'plot.window'
diagplot.ftd: no visible global function definition for 'axis'
diagplot.ftd: no visible global function definition for 'lines'
diagplot.ftd: no visible global function definition for 'grid'
diagplot.ftd: no visible global function definition for 'title'
diagplot.mds: no visible global function definition for 'as.dist'
diagplot.mds: no visible global function definition for 'cor'
diagplot.mds: no visible global function definition for 'cmdscale'
diagplot.mds: no visible global function definition for 'plot'
diagplot.mds: no visible global function definition for 'text'
diagplot.mds: no visible global function definition for 'grid'
diagplot.noiseq: no visible global function definition for 'grid'
diagplot.noiseq: no visible global function definition for 'new'
diagplot.noiseq : <anonymous>: no visible global function definition
  for 'quantile'
diagplot.noiseq.saturation: no visible global function definition for
  'par'
diagplot.noiseq.saturation: no visible global function definition for
  'plot.new'
diagplot.noiseq.saturation: no visible global function definition for
  'plot.window'
diagplot.noiseq.saturation: no visible global function definition for
  'axis'
diagplot.noiseq.saturation: no visible global function definition for
  'title'
diagplot.noiseq.saturation: no visible global function definition for
  'lines'
diagplot.noiseq.saturation: no visible global function definition for
  'points'
diagplot.noiseq.saturation: no visible global function definition for
  'grid'
diagplot.noiseq.saturation: no visible global function definition for
  'mtext'
diagplot.pairs: no visible global function definition for 'par'
diagplot.pairs: no visible global function definition for 'plot'
diagplot.pairs: no visible global function definition for 'text'
diagplot.pairs: no visible global function definition for 'arrows'
diagplot.pairs: no visible global function definition for 'lines'
diagplot.pairs: no visible global function definition for 'cor'
diagplot.roc: no visible global function definition for 'par'
diagplot.roc: no visible global function definition for 'plot.new'
diagplot.roc: no visible global function definition for 'plot.window'
diagplot.roc: no visible global function definition for 'axis'
diagplot.roc: no visible global function definition for 'lines'
diagplot.roc: no visible global function definition for 'grid'
diagplot.roc: no visible global function definition for 'title'
diagplot.venn: no visible global function definition for 'runif'
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'
diagplot.volcano: no visible global function definition for 'runif'
diagplot.volcano: no visible global function definition for 'par'
diagplot.volcano: no visible global function definition for 'plot.new'
diagplot.volcano: no visible global function definition for
  'plot.window'
diagplot.volcano: no visible global function definition for 'axis'
diagplot.volcano: no visible global function definition for 'title'
diagplot.volcano: no visible global function definition for 'points'
diagplot.volcano: no visible global function definition for 'abline'
diagplot.volcano: no visible global function definition for 'grid'
estimate.aufc.weights: no visible global function definition for
  'runif'
estimate.aufc.weights : <anonymous>: no visible global function
  definition for 'rollmean'
estimate.sim.params : <anonymous>: no visible global function
  definition for 'var'
estimate.sim.params : <anonymous>: no visible global function
  definition for 'optimize'
estimate.sim.params: no visible global function definition for
  'dev.new'
estimate.sim.params: no visible global function definition for 'plot'
estimate.sim.params: no visible global function definition for 'title'
estimate.sim.params: no visible global function definition for 'grid'
filter.genes: no visible binding for global variable 'quantile'
filter.genes: no visible global function definition for 'median'
filter.genes: no visible global function definition for 'quantile'
fisher.method: no visible global function definition for 'pchisq'
fisher.method: no visible global function definition for 'p.adjust'
fisher.method.perm : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for 'na.exclude'
fisher.method.perm: no visible global function definition for
  'p.adjust'
get.defaults: no visible binding for global variable 'median'
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 'start'
get.ucsc.annotation: no visible global function definition for 'end'
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'
graphics.close: no visible global function definition for 'dev.off'
graphics.open: no visible global function definition for 'dev.new'
graphics.open: no visible global function definition for 'pdf'
graphics.open: no visible global function definition for 'postscript'
graphics.open: no visible global function definition for 'png'
graphics.open: no visible global function definition for 'jpeg'
graphics.open: no visible global function definition for 'bmp'
graphics.open: no visible global function definition for 'tiff'
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.sim.data.sd: no visible global function definition for 'runif'
make.sim.data.sd: no visible global function definition for 'rnbinom'
make.sim.data.sd: no visible global function definition for 'rexp'
make.sim.data.tcc: no visible global function definition for 'runif'
make.stat : <anonymous>: no visible global function definition for
  'median'
make.stat : <anonymous>: no visible global function definition for 'sd'
make.stat : <anonymous>: no visible global function definition for
  'mad'
meta.perm : <anonymous>: no visible global function definition for
  'runif'
meta.perm: no visible global function definition for 'mclapply'
meta.test : <anonymous>: no visible binding for global variable
  'combine.test'
metaseqr: no visible binding for global variable 'p.adjust.methods'
metaseqr : <anonymous>: no visible binding for global variable
  'p.adjust'
metaseqr : <anonymous>: no visible global function definition for
  'p.adjust'
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 'start'
read2count: no visible global function definition for 'end'
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
  'as'
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.bayseq: no visible global function definition for 'new'
stat.deseq: no visible global function definition for 'sizeFactors<-'
stat.edger: no visible global function definition for 'model.matrix'
stat.edger: possible error in glmLRT(fit, contrast = co, test =
  stat.args$test): unused argument (test = stat.args$test)
stat.limma: no visible global function definition for 'model.matrix'
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'
wp.adjust: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  AnnotatedDataFrame BamFile DataFrame GRanges IRanges Rle ScanBamParam
  abline alphabetFrequency arrows as as.dist asBam assayData assays
  axis biocLite bmp cmdscale colorRampPalette combine.test cor countBam
  countOverlaps dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable
  dev.new dev.off draw.pairwise.venn draw.quad.venn draw.quintuple.venn
  draw.triple.venn end getBSgenome getSeq grid import.bed
  installed.genomes jpeg ks.test lines mad makeGRangesFromDataFrame
  mclapply mcols<- median model.matrix mtext na.exclude nams new
  optimize p.adjust p.adjust.methods par pchisq pdf plot plot.new
  plot.window png points postscript quantile readGAlignments reduce
  rexp rnbinom rollmean runif scanBamFlag sd seqlevels seqnames
  sizeFactors<- start strand strand<- summarizeOverlaps text tiff title
  var
Consider adding
  importFrom("grDevices", "bmp", "colorRampPalette", "dev.new",
             "dev.off", "jpeg", "pdf", "png", "postscript", "tiff")
  importFrom("graphics", "abline", "arrows", "axis", "grid", "lines",
             "mtext", "par", "plot", "plot.new", "plot.window", "points",
             "text", "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test",
             "mad", "median", "model.matrix", "na.exclude", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "quantile",
             "rexp", "rnbinom", "runif", "sd", "start", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
diagplot.de.heatmap 9.02   0.11    9.12
diagplot.volcano    5.75   0.02    5.77
diagplot.filtered   1.76   0.33    5.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
diagplot.de.heatmap 10.41   0.09   10.50
diagplot.volcano     6.77   0.01    6.79
diagplot.filtered    2.00   0.11    5.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/metaseqR.Rcheck/00check.log'
for details.

metaseqR.Rcheck/00install.out:


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_1.16.0.zip
* DONE (metaseqR)

metaseqR.Rcheck/examples_i386/metaseqR-Ex.timings:

nameusersystemelapsed
as.class.vector000
build.export000
calc.f1score000
calc.otr000
check.contrast.format000
check.file.args000
check.libsize000
check.num.args0.060.000.06
check.packages000
check.parallel000
check.text.args000
combine.bonferroni000
combine.maxp000
combine.minp000
combine.simes000
combine.weight000
construct.gene.model000
diagplot.avg.ftd0.320.010.35
diagplot.boxplot1.530.111.71
diagplot.cor1.130.051.18
diagplot.de.heatmap9.020.119.12
diagplot.edaseq2.280.202.49
diagplot.filtered1.760.335.95
diagplot.ftd0.050.030.08
diagplot.mds1.230.001.23
diagplot.metaseqr1.390.051.44
diagplot.noiseq1.740.061.81
diagplot.pairs3.000.023.02
diagplot.roc0.030.010.04
diagplot.venn0.280.030.52
diagplot.volcano5.750.025.77
disp000
downsample.counts000
estimate.aufc.weights000
estimate.sim.params000
filter.exons000
filter.genes000
filter.high0.010.000.02
filter.low0.020.000.01
fisher.method0.090.000.10
fisher.method.perm0.080.000.08
fisher.sum000
get.annotation000
get.arg000
get.biotypes000
get.bs.organism000
get.dataset000
get.defaults000
get.ensembl.annotation000
get.exon.attributes000
get.gc.content000
get.gene.attributes000
get.host000
get.preset.opts000
get.strict.biofilter000
get.ucsc.annotation000
get.ucsc.credentials000
get.ucsc.dbl000
get.ucsc.organism000
get.ucsc.query000
get.ucsc.tabledef0.020.000.02
get.ucsc.tbl.tpl000
get.valid.chrs0.010.000.01
get.weights000
graphics.close000
graphics.open000
load.bs.genome000
make.avg.expression000
make.contrast.list000
make.fold.change000
make.grid000
make.html.body000
make.html.cells000
make.html.header000
make.html.rows000
make.html.table000
make.matrix000
make.permutation000
make.sample.list0.020.000.02
make.sim.data.sd000
make.sim.data.tcc000
make.stat000
make.transformation000
make.venn.areas000
make.venn.colorscheme000
make.venn.counts000
make.venn.pairs000
meta.perm000
meta.test000
meta.worker000
metaseqr0.020.000.02
mlfo000
normalize.deseq000
normalize.edaseq000
normalize.edger000
normalize.nbpseq000
normalize.noiseq0.020.000.02
read.targets000
read2count000
reduce.exons000
reduce.gene.data000
set.arg000
stat.bayseq000
stat.deseq000
stat.edger000
stat.limma000
stat.nbpseq000
stat.noiseq000
validate.alg.args0.020.000.02
validate.list.args000
wapply000

metaseqR.Rcheck/examples_x64/metaseqR-Ex.timings:

nameusersystemelapsed
as.class.vector000
build.export000
calc.f1score0.010.000.01
calc.otr000
check.contrast.format000
check.file.args000
check.libsize000
check.num.args0.050.000.05
check.packages000
check.parallel000
check.text.args000
combine.bonferroni000
combine.maxp000
combine.minp000
combine.simes000
combine.weight000
construct.gene.model000
diagplot.avg.ftd0.930.000.95
diagplot.boxplot1.690.081.76
diagplot.cor1.200.021.22
diagplot.de.heatmap10.41 0.0910.50
diagplot.edaseq1.430.061.50
diagplot.filtered2.000.115.97
diagplot.ftd0.020.040.12
diagplot.mds1.330.011.34
diagplot.metaseqr1.750.061.81
diagplot.noiseq2.670.112.82
diagplot.pairs2.800.102.89
diagplot.roc0.050.000.11
diagplot.venn0.500.030.53
diagplot.volcano6.770.016.79
disp000
downsample.counts000
estimate.aufc.weights000
estimate.sim.params000
filter.exons000
filter.genes000
filter.high0.000.020.02
filter.low0.010.000.01
fisher.method0.080.000.08
fisher.method.perm0.060.000.06
fisher.sum000
get.annotation000
get.arg000
get.biotypes000
get.bs.organism000
get.dataset000
get.defaults000
get.ensembl.annotation000
get.exon.attributes000
get.gc.content000
get.gene.attributes000
get.host000
get.preset.opts000
get.strict.biofilter000
get.ucsc.annotation000
get.ucsc.credentials000
get.ucsc.dbl000
get.ucsc.organism000
get.ucsc.query000
get.ucsc.tabledef000
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