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CHECK report for GGtools on merida2

This page was generated on 2019-04-09 13:23:32 -0400 (Tue, 09 Apr 2019).

Package 668/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGtools 5.19.0
VJ Carey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GGtools
Branch: master
Last Commit: 76c00c1
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: GGtools
Version: 5.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GGtools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GGtools_5.19.0.tar.gz
StartedAt: 2019-04-09 01:12:59 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:27:46 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 887.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GGtools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GGtools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GGtools_5.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘5.19.0’
* 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 71.9Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    data   27.0Mb
    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.
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
plot,gwSnpScreenResult-character: warning in axis(3, at =
  genePosition(x@gene, annlib = x@annotation), col = "red", lwd = 2,
  label = " "): partial argument match of 'label' to 'labels'
.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'
SnpMatrixCisToSummex: no visible global function definition for
  'rowRanges'
add878: no visible binding for global variable 'hmm878'
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 : .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'
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 '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'
eqtlTests.me: no visible binding for global variable 'modelLINEAR'
eqtlTests.me: no visible binding for global variable 'SlicedData'
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'
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'
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'
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<-'
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'
Undefined global functions or variables:
  %dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData
  as.data.table assay assays bindcadd bindmaf chi.squared colData curp
  detectCores excl export.gff3 firstHalf firstThird foreach forestplot
  gwastagger gwrngs hg19.si.df hmm878 i i1 i2 lastThird maf mafs
  mclapply midThird modelLINEAR npc overlapsAny pl radiusUsed ranges<-
  rowRanges runOneSplit select setkey setkeyv setnames snp snpcount
  snpsBySeqname target tileGenome value wald.test x
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
cisAssoc  59.731  2.471  62.687
eqtlTests 10.207  0.429  10.775
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/00check.log’
for details.



Installation output

GGtools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GGtools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GGtools’ ...
** R
** data
** inst
** byte-compile and prepare 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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
116.635  10.596 111.836 

GGtools.Rcheck/tests/eqvgwst.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, 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 
 25.006   1.223  26.436 

GGtools.Rcheck/tests/test.meqtlTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, 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/RtmpOQVdzy"

- 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 /Users/biocbuild/bbs-3.9-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 
 28.998   1.317  30.636 

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


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  0.266   0.071   0.304 

GGtools.Rcheck/tests/testCisMap.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, 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 
 52.405   3.937  56.804 

GGtools.Rcheck/tests/testTrans.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 /Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests/cisScratch22/tsc_20_chr22.ff
2opening ff /Users/biocbuild/bbs-3.9-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 
126.432   4.912 142.326 

Example timings

GGtools.Rcheck/GGtools-Ex.timings

nameusersystemelapsed
All.cis0.0000.0010.001
CisConfig-class0.0030.0010.004
EqAppr-class000
GGtools-package0.0010.0010.000
TransConfig-class0.0020.0000.003
b10.0840.0030.088
best.cis.eQTLs0.0010.0010.002
best.trans.eQTLs000
bindmaf0.0000.0000.001
cgff2dt0.0320.0010.033
cisAssoc59.731 2.47162.687
cisRun-class0.0010.0010.002
ciseqByCluster0.0010.0000.000
collectBest0.0000.0010.001
concatCis000
eqBox3.0190.1193.164
eqsens_dt0.0000.0010.001
eqtlTests10.207 0.42910.775
eqtlTests.me0.0010.0000.001
eqtlTestsManager-class0.0010.0000.001
ex2.5620.0982.707
getCisMap0.0010.0000.000
gwSnpTests3.2860.1073.482
hmm8780.8820.0350.945
pifdr0.8230.0460.940
qqhex0.0880.0170.107
sampsInVCF0.0570.0010.058
sensiCisInput-class0.0010.0010.001
sensiCisOutput-class0.0000.0000.001
simpleTiling000
snplocsDefault000
strMultPop0.0680.0220.091
transManager-class0.0000.0010.000
transScores000
vcf2sm0.0960.0030.100