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CHECK report for GGtools on malbec1

This page was generated on 2018-04-12 13:07:45 -0400 (Thu, 12 Apr 2018).

Package 584/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGtools 5.14.0
VJ Carey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GGtools
Branch: RELEASE_3_6
Last Commit: bf79a26
Last Changed Date: 2017-10-30 12:39:17 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GGtools
Version: 5.14.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GGtools_5.14.0.tar.gz
StartedAt: 2018-04-11 23:54:58 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-12 00:05:53 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 654.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GGtools_5.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘5.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘MatrixEQTL’
* 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 ‘GGtools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 73.0Mb
  sub-directories of 1Mb or more:
    data   27.0Mb
    doc     1.6Mb
    parts   2.0Mb
    pup     2.0Mb
    rdas   10.3Mb
    vcf    28.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'Homo.sapiens' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Homo.sapiens' 'parallel'
  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
.calfig: no visible global function definition for 'axis'
.calfig: no visible global function definition for 'points'
.calfig: no visible global function definition for 'text'
.calfig: no visible global function definition for 'abline'
.summarize: no visible global function definition for 'ftable'
.summarize: no visible binding for global variable 'npc'
.summarize: no visible binding for global variable 'maf'
.summarize: no visible binding for global variable 'radiusUsed'
.summarize: no visible binding for global variable 'excl'
.transTab: no visible global function definition for 'snpsBySeqname'
All.cis.eQTLs: no visible global function definition for 'approx'
SnpMatrixCisToSummex: no visible global function definition for
  'rowRanges'
add878: no visible binding for global variable 'hmm878'
add878: no visible global function definition for 'relevel'
addcadd: no visible binding for global variable 'bindcadd'
addcadd: no visible global function definition for '%dopar%'
addcadd: no visible global function definition for 'foreach'
addcadd: no visible binding for global variable 'x'
addgwhit: no visible binding for global variable 'gwastagger'
addgwhit: no visible global function definition for 'overlapsAny'
appraise : <anonymous>: no visible global function definition for
  'relevel'
appraise : .redu.fdr: no visible global function definition for
  'setkey'
appraise : .redu.fdr: no visible binding for global variable 'snp'
appraise : .redu.fdr: no visible binding for global variable '.N'
appraise : .redu.fdr : <anonymous>: no visible global function
  definition for 'setkeyv'
appraise : .redu.fdr : <anonymous>: no visible binding for global
  variable '.N'
appraise : .discmods: no visible global function definition for
  '%dopar%'
appraise : .discmods: no visible global function definition for
  'foreach'
appraise : .discmods: no visible global function definition for
  'binomial'
appraise : .discmods: no visible global function definition for
  'predict'
appraise : .discmods: no visible global function definition for 'coef'
appraise : .discmods: no visible global function definition for 'vcov'
appraise : .discmods: no visible global function definition for
  'model.matrix'
appraise : .discmods: no visible global function definition for
  'plogis'
binnedQQ: no visible global function definition for 'par'
binnedQQ: no visible global function definition for 'qqplot'
binnedQQ: no visible global function definition for 'mtext'
binqq: no visible global function definition for 'text'
binqq: no visible global function definition for 'segments'
binqq: no visible global function definition for 'abline'
binqq: no visible global function definition for 'axis'
buildConfList : z : <anonymous>: no visible binding for global variable
  'pl'
cgff2dt: no visible global function definition for '%dopar%'
cgff2dt: no visible global function definition for 'foreach'
cgff2dt: no visible global function definition for 'as.data.table'
cgff2dt: no visible binding for global variable 'hmm878'
cgff2dt: no visible global function definition for 'overlapsAny'
cgff2dt: no visible binding for global variable 'gwastagger'
cisAssoc: no visible global function definition for 'rowRanges'
cisAssoc: no visible global function definition for 'assays'
cisAssoc: no visible global function definition for 'as.formula'
cisAssoc: no visible global function definition for 'runif'
cisAssoc: no visible global function definition for 'colData'
cisAssoc: no visible binding for global variable 'chi.squared'
ciseqByCluster : <anonymous>: no visible global function definition for
  'detectCores'
ciseqByCluster: no visible binding for '<<-' assignment to 'firstHalf'
ciseqByCluster: no visible binding for '<<-' assignment to 'secondHalf'
ciseqByCluster: no visible binding for '<<-' assignment to 'firstThird'
ciseqByCluster: no visible binding for '<<-' assignment to 'lastThird'
ciseqByCluster: no visible binding for '<<-' assignment to 'midThird'
ciseqByCluster : setupSplit : <anonymous>: no visible binding for
  global variable 'mclapply'
ciseqByCluster: no visible binding for '<<-' assignment to
  'runOneSplit'
ciseqByCluster : <anonymous>: no visible binding for global variable
  'firstHalf'
ciseqByCluster : <anonymous> : cr2gff: no visible global function
  definition for 'ranges<-'
ciseqByCluster : <anonymous> : cr2gff: no visible global function
  definition for 'export.gff3'
ciseqByCluster: no visible binding for global variable 'firstThird'
ciseqByCluster: no visible binding for global variable 'midThird'
ciseqByCluster: no visible binding for global variable 'lastThird'
ciseqByCluster : <anonymous>: no visible global function definition for
  'runOneSplit'
eqBox: no visible global function definition for 'assay'
eqDesc: no visible global function definition for 'assay'
eqsens_dt: no visible global function definition for 'setnames'
eqsens_dt: no visible global function definition for '%dopar%'
eqsens_dt: no visible global function definition for 'foreach'
eqsens_dt: no visible binding for global variable 'curp'
eqtlEstimates : <anonymous>: no visible global function definition for
  'formula'
eqtlTests : <anonymous>: no visible global function definition for
  'formula'
eqtlTests.me: no visible binding for global variable 'modelLINEAR'
eqtlTests.me: no visible binding for global variable 'SlicedData'
eqtlTests.me: no visible global function definition for 'model.matrix'
eqtlTests.me: no visible binding for global variable
  'Matrix_eQTL_engine'
eqtlTests.meText: no visible binding for global variable 'modelLINEAR'
eqtlTests.meText: no visible binding for global variable 'SlicedData'
eqtlTests.meText: no visible binding for global variable
  'Matrix_eQTL_engine'
eqtlTests2 : <anonymous>: no visible global function definition for
  'formula'
fplot: no visible global function definition for 'forestplot'
genemodel: no visible global function definition for 'select'
genemodel: no visible binding for global variable 'Homo.sapiens'
get.dffits : maxdf: no visible global function definition for 'dffits'
get.dffits : <anonymous>: no visible global function definition for
  'lm'
getAsSlicedData: no visible binding for global variable 'target'
getCisMap: no visible global function definition for 'snpsBySeqname'
get_probechunks: no visible global function definition for 'select'
inflammFilter: no visible binding for global variable 'gwrngs'
inflammFilter: no visible global function definition for 'overlapsAny'
makeSeqinfo: no visible binding for global variable 'hg19.si.df'
meqtlTests : gfun: no visible global function definition for 'formula'
pifdr: no visible global function definition for 'hist'
pifdr.old: no visible global function definition for 'approx'
plotsens: no visible binding for global variable 'mafs'
plotsens: no visible binding for global variable 'value'
plotsens: no visible binding for global variable 'FDR'
pullHits: no visible global function definition for 'ranges<-'
qqhex: no visible global function definition for 'qqplot'
richNull : <anonymous>: no visible global function definition for
  'bindmaf'
simpleTiling: no visible binding for global variable 'Homo.sapiens'
simpleTiling: no visible global function definition for 'tileGenome'
topKfeats: no visible binding for global variable 'i1'
topKfeats: no visible binding for global variable 'i2'
tscan2df: no visible global function definition for '%dopar%'
tscan2df: no visible global function definition for 'foreach'
tscan2df: no visible binding for global variable 'i'
tscan2gr: no visible global function definition for '%dopar%'
tscan2gr: no visible global function definition for 'foreach'
tscan2gr: no visible binding for global variable 'i'
waldtests : <anonymous>: no visible global function definition for
  'wald.test'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'snpcount'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'snpsBySeqname'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'pos'
plot,gwSnpScreenResult-character: no visible binding for global
  variable 'smoothScatter'
plot,gwSnpScreenResult-character: no visible global function definition
  for 'axis'
Undefined global functions or variables:
  %dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData abline
  approx as.data.table as.formula assay assays axis bindcadd bindmaf
  binomial chi.squared coef colData curp detectCores dffits excl
  export.gff3 firstHalf firstThird foreach forestplot formula ftable
  gwastagger gwrngs hg19.si.df hist hmm878 i i1 i2 lastThird lm maf
  mafs mclapply midThird model.matrix modelLINEAR mtext npc overlapsAny
  par pl plogis points pos predict qqplot radiusUsed ranges<- relevel
  rowRanges runOneSplit runif segments select setkey setkeyv setnames
  smoothScatter snp snpcount snpsBySeqname target text tileGenome value
  vcov wald.test x
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "mtext", "par",
             "points", "segments", "smoothScatter", "text")
  importFrom("stats", "approx", "as.formula", "binomial", "coef",
             "dffits", "formula", "ftable", "lm", "model.matrix",
             "plogis", "predict", "qqplot", "relevel", "runif", "vcov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘MatrixEQTL’
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
cisAssoc  39.292  1.460  40.797
eqtlTests  7.712  0.348   8.104
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘cis.R’
  Running ‘eqvgwst.R’
  Running ‘test.meqtlTests.R’
  Running ‘test.meta.trans.R’
  Running ‘testCisMap.R’
  Running ‘testTrans.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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/00check.log’
for details.



Installation output

GGtools.Rcheck/00install.out

* installing *source* package ‘GGtools’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GGtools)

Tests output

GGtools.Rcheck/tests/cis.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> suppressPackageStartupMessages(library(GGtools))
> 
> # configure
>    cc = new("CisConfig")
>    chrnames(cc) = "21"
>    genome(cc) = "hg19"
>    nperm(cc) = 2L
>    lkp = try(library(parallel))
>    if (!inherits(lkp, "try-error")) {
+       nc = min(10, detectCores())
+       options(mc.cores=nc)
+       geneApply(cc) = mclapply
+       }
>    estimates(cc) = FALSE
>    set.seed(1234)
> #   system.time(f1 <- cisScores( cc ))
>  #
>  # demonstrate adding annotation on chromatin state and gwas status
>  #
>  eprops = function(ans) {
+  #
+  # only adds fields to values() of the input
+  #
+   data(hmm878)
+   ac = as.character
+   eqr = GRanges(ac(seqnames(ans)), IRanges(ans$snplocs, width=1))
+   fo = findOverlaps(eqr, hmm878)
+   chromcat878 = factor(rep("none", length(ans)), levels=c(unique(hmm878$name), "none"))
+   chromcat878[ queryHits(fo) ] = factor(hmm878$name[subjectHits(fo)])
+   ans$chromcat878 = chromcat878
+  
+   if (require(gwascat)) {
+     data(gwastagger)
+     isgwashit = 1*(overlapsAny(eqr, gwastagger) | ans$snp %in% gwastagger$tagid) # allow match by loc or name
+     ans$isgwashit = isgwashit
+     }
+   ans
+  }
>  extraProps(cc) = eprops
>  set.seed(1234)
>  rhs(cc) = ˜1-1
> if (.Platform$OS.type != "windows") {
+  (f2 <- cisScores( cc ))
+  isTRUE(sum(f2$fdr < 0.05) == 172)  # can change with annotation or location changes, check serialized results if necessary
+ }
get data...build map...

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

NOTE: expanding gene ranges by radius 50000 leads to negative start positions that are reset to 1.
run smFilter...filter probes in map...tests...get data...build map...run smFilter...filter probes in map...tests...get data...build map...run smFilter...filter probes in map...tests...Loading required package: gwascat
gwascat loaded.  Use data(ebicat38) for hg38 coordinates;
 data(ebicat37) for hg19 coordinates.
[1] FALSE
> TRUE
[1] TRUE
> 
> proc.time()
   user  system elapsed 
101.600  11.296  99.577 

GGtools.Rcheck/tests/eqvgwst.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> # april 2011/jan 2012
> # compares gwSnpTests to eqtlTests
> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> hmceuB36.2021 <- getSS("GGtools", c("20"))
> library(illuminaHumanv1.db)

> cp = get("CPNE1", revmap(illuminaHumanv1SYMBOL))
> hcp = hmceuB36.2021[ probeId(cp), ]
> t1 = gwSnpTests(genesym("CPNE1")˜male, hcp)
> pick = as(t1@.Data[[1]], "data.frame")[22101:22115,]
> rsids = rownames(pick)[!is.na(pick[,1])]
> csq = pick[rsids,1]
> names(csq) = rsids
> fi = tempfile()
> if (file.exists(fi)) unlink(fi, recursive=TRUE)
> t2 = eqtlTests(hcp, ˜male, targdir=fi)
> sco = t2[rsids,][,1]
> unlink(fi, recursive=TRUE)
> comp = (sco-trunc(100*csq,0)/100)/sco
> (!(max(abs(comp)) > .01))
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
 19.148   0.452  20.049 

GGtools.Rcheck/tests/test.meqtlTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> library(ff)
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:data.table':

    setattr

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpyDnqX7"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

> 
> tenOn2021 =
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S")
> 
> c22 = getSS("GGdata", "22")
> c22 = c22[probeId(tenOn2021),]
> 
> e1 = eqtlTests(c22, ˜1, targdir = "ooo")
> m1 = meqtlTests(list(c22, c22), list(˜1, ˜1), targdir = "ooobb")
> 
> ae = as.ram(e1@fffile)
opening ff /home/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/tests/ooo/foo_chr22.ff
> am = as.ram(m1@fffile)
> all.equal(as.numeric(ae)*2 ,as.numeric(am) )
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
 22.436   0.608  23.532 

GGtools.Rcheck/tests/test.meta.trans.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> heavyTest = function() {
+ library(GGtools)
+ 
+ # verifies that transScores agrees with snp.rhs.tests to obtain best
+ # trans scores
+ 
+ tenOn2021 = 
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") 
+ 
+ suppressPackageStartupMessages(library(GGtools))
+ 
+ mt1 = meta.transScores(c("GGdata", "GGdata"), rhs=list(˜1, ˜1), snpchr="22", chrnames=as.character(c(20,21)),
+ #
+ # all tests are trans, to verify buffering approach
+ #
+         radius = 2e+06,  K=4, targdir="uiu2",
+     probesToKeep = tenOn2021, batchsize = 200, 
+     geneannopk = "illuminaHumanv1.db", 
+     snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", SMFilterList = list( function(x) x[probeId(tenOn2021),],
+          function(x) x[probeId(tenOn2021), ]),
+     schrpref = "ch", exFilter = list( function(x) x, function(x) x)) 
+ 
+ transTab(mt1)
+ }
> 
> proc.time()
   user  system elapsed 
  0.156   0.020   0.172 

GGtools.Rcheck/tests/testCisMap.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (.Platform$OS.type != "windows") {
+ t20 = GGtools:::getCisMap()
+ 
+ NL = GGtools:::namelist(t20)
+ 
+ NL1 = NL[[1]]
+ 
+ t20sl = t20@snplocs[NL1]
+ 
+ probe1 = names(NL)[1]
+ 
+ TARG = t20@generanges[probe1]-50000
+ 
+ d = distance(TARG, t20sl)
+ 
+ all(d <= 50000)
+ } else TRUE

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid




Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

NOTE: expanding gene ranges by radius 50000 leads to negative start positions that are reset to 1.
[1] TRUE
> 
> proc.time()
   user  system elapsed 
 46.792   1.852  49.288 

GGtools.Rcheck/tests/testTrans.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # verifies that transScores agrees with snp.rhs.tests to obtain best
> # trans scores
> 
> suppressPackageStartupMessages(library(GGtools))
> 
> tenOn2021 = 
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") 
> 
> tconf = new("TransConfig")
> radius(tconf) = 2000000L
> smpack(tconf) = "GGdata"
> rhs(tconf) = ˜1
> snpchr(tconf) = "22"  # we get scores for all SNP on this chrom
> chrnames(tconf) = c("20", "21")
> gbufsize(tconf) = 4L
> smFilter(tconf) = function(x) x[probeId(tenOn2021),]
> snpannopk(tconf) = snplocsDefault()
> schrpref(tconf) = "ch"
> exFilter(tconf) = function(x)x
> gchrpref = ""
> batchsize(tconf) = 200L
> 
> suppressPackageStartupMessages(library(GGtools))
> 
> t1 = transScores(tconf)
Loading required package: illuminaHumanv1.db

opening ff /home/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/tests/cisScratch22/tsc_20_chr22.ff
2opening ff /home/biocbuild/bbs-3.6-bioc/meat/GGtools.Rcheck/tests/cisScratch22/tsctmp2_chr22.ff
> 
> #"GGdata", rhs=˜1, snpchr="22", chrnames=as.character(c(20,21)),
> #
> # all tests are trans, to verify buffering approach
> #
> #        radius = 2e+06,  K=4,
> #    probesToKeep = tenOn2021, batchsize = 200, 
> #    geneannopk = "illuminaHumanv1.db", 
> #    snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", 
> #    schrpref = "ch", exFilter = function(x) x) 
> 
> if (.Platform$OS.type != "windows") {
+   tt1 = transTab(t1)
+   
+   cleanup_transff = function(x) {
+    fn = attr(attr(x@base$scores, "physical"), "filename")
+    comps = strsplit(fn, "/")[[1]]
+    nel = length(comps)
+    unlink(comps[nel-1], recursive=TRUE)
+   }
+   
+   cleanup_transff(t1)
+   
+   c22 = getSS("GGdata", "22")
+   
+   exl = lapply(tenOn2021, function(x) exprs(c22)[x,])
+   rhst = lapply(1:length(exl), function(g) {
+        ex = exl[[g]]
+        snp.rhs.tests(ex˜1, snp.data=smList(c22)[[1]], fam="gaussian", uncertain=TRUE) })
+   csnp1 = sapply(rhst, function(x)chi.squared(x)[1])
+   csnp50 = sapply(rhst, function(x)chi.squared(x)[50])
+   
+   
+   #all(abs(floor(sort(csnp1, decreasing=TRUE)[1:4]*10)/10 - tt1[1:4,2]) < .01)
+   #all(abs(floor(sort(csnp50, decreasing=TRUE)[1:4]*10)/10 - tt1[197:200,2]) < 0.01)
+   
+   ttdt = data.table(tt1)
+   SS = sort(sapply(rhst, function(x) max(chi.squared(x), na.rm=TRUE))) 
+   TT = sort(ttdt[,max(chisq),by="probeid"]$V1) 
+   maxchk = (max(abs(SS-TT))<.01)
+   
+   # needs more work, tt1 is organized by snp
+   #SS = sort(sapply(rhst, function(x) min(chi.squared(x), na.rm=TRUE))) 
+   #TT = sort(ttdt[,min(chisq),by="probeid"]$V1) 
+   #minchk = (max(abs(SS-TT))<.01)
+   
+   maxchk 
+ }
Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh37
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
[1] TRUE
>   
> 
> proc.time()
   user  system elapsed 
 92.748   2.228  95.653 

Example timings

GGtools.Rcheck/GGtools-Ex.timings

nameusersystemelapsed
All.cis0.0000.0000.001
CisConfig-class0.0040.0000.002
EqAppr-class0.0040.0000.001
GGtools-package000
TransConfig-class0.0000.0000.001
b10.1280.0000.131
best.cis.eQTLs0.0000.0000.001
best.trans.eQTLs0.0000.0000.001
bindmaf0.0040.0000.001
cgff2dt0.0160.0000.015
cisAssoc39.292 1.46040.797
cisRun-class0.0040.0000.001
ciseqByCluster000
collectBest0.0000.0000.002
concatCis000
eqBox2.2240.0922.319
eqsens_dt0.0000.0000.001
eqtlTests7.7120.3488.104
eqtlTests.me0.0000.0000.001
eqtlTestsManager-class0.0040.0000.001
ex2.2800.0482.329
getCisMap000
gwSnpTests2.9360.1403.083
hmm8780.5800.0080.587
pifdr1.2000.1001.329
qqhex0.0800.0080.088
sampsInVCF0.040.000.04
sensiCisInput-class0.0000.0000.001
sensiCisOutput-class000
simpleTiling000
snplocsDefault0.0000.0000.001
strMultPop0.0680.0000.069
transManager-class0.0000.0000.001
transScores000
vcf2sm0.0680.0000.067