VJ Carey
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GGtools |
| Branch: RELEASE_3_9 |
| Last Commit: 189a896 |
| Last Changed Date: 2019-05-02 11:53:06 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:46:06 -0400 (Wed, 16 Oct 2019).
| Package 677/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GGtools 5.20.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: GGtools |
| Version: 5.20.0 |
| 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_5.20.0.tar.gz |
| StartedAt: 2019-10-16 03:15:01 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:36:54 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1313.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GGtools.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_5.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘5.20.0’
* 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 : : no visible global function
definition for 'setkeyv'
appraise : .redu.fdr : : 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 : : 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 : : 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 : : no visible binding for
global variable 'mclapply'
ciseqByCluster: no visible binding for '<<-' assignment to
'runOneSplit'
ciseqByCluster : : no visible binding for global variable
'firstHalf'
ciseqByCluster : : cr2gff: no visible global function
definition for 'ranges<-'
ciseqByCluster : : 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 : : 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 : : 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 : : 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 65.208 4.452 69.701
eqtlTests 10.638 0.818 11.473
* 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.
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’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GGtools)
GGtools.Rcheck/tests/cis.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
176.715 23.007 178.340
GGtools.Rcheck/tests/eqvgwst.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 object is masked from 'package:Matrix':
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, 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, 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
32.583 2.677 35.217
GGtools.Rcheck/tests/test.meqtlTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 object is masked from 'package:Matrix':
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, 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, 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/RtmpZIGoLi"
- 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
36.792 2.861 39.612
GGtools.Rcheck/tests/test.meta.trans.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
0.399 0.148 0.490
GGtools.Rcheck/tests/testCisMap.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, 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, 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
89.767 8.445 108.354
GGtools.Rcheck/tests/testTrans.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
178.368 9.451 193.977
GGtools.Rcheck/GGtools-Ex.timings
| name | user | system | elapsed | |
| All.cis | 0.001 | 0.001 | 0.001 | |
| CisConfig-class | 0.004 | 0.002 | 0.005 | |
| EqAppr-class | 0.001 | 0.001 | 0.001 | |
| GGtools-package | 0.001 | 0.000 | 0.001 | |
| TransConfig-class | 0.003 | 0.001 | 0.004 | |
| b1 | 0.104 | 0.005 | 0.108 | |
| best.cis.eQTLs | 0.001 | 0.001 | 0.002 | |
| best.trans.eQTLs | 0.000 | 0.000 | 0.001 | |
| bindmaf | 0.001 | 0.000 | 0.001 | |
| cgff2dt | 0.028 | 0.002 | 0.030 | |
| cisAssoc | 65.208 | 4.452 | 69.701 | |
| cisRun-class | 0.001 | 0.001 | 0.003 | |
| ciseqByCluster | 0 | 0 | 0 | |
| collectBest | 0.001 | 0.001 | 0.001 | |
| concatCis | 0.001 | 0.000 | 0.001 | |
| eqBox | 3.465 | 0.273 | 3.739 | |
| eqsens_dt | 0 | 0 | 0 | |
| eqtlTests | 10.638 | 0.818 | 11.473 | |
| eqtlTests.me | 0.001 | 0.001 | 0.002 | |
| eqtlTestsManager-class | 0.001 | 0.001 | 0.002 | |
| ex | 2.786 | 0.195 | 2.981 | |
| getCisMap | 0.000 | 0.001 | 0.001 | |
| gwSnpTests | 3.383 | 0.181 | 3.564 | |
| hmm878 | 0.597 | 0.057 | 0.654 | |
| pifdr | 0.906 | 0.090 | 0.996 | |
| qqhex | 0.100 | 0.016 | 0.119 | |
| sampsInVCF | 0.112 | 0.002 | 0.115 | |
| sensiCisInput-class | 0.001 | 0.001 | 0.002 | |
| sensiCisOutput-class | 0.001 | 0.001 | 0.002 | |
| simpleTiling | 0.001 | 0.001 | 0.001 | |
| snplocsDefault | 0.001 | 0.001 | 0.001 | |
| strMultPop | 0.090 | 0.036 | 0.126 | |
| transManager-class | 0.001 | 0.001 | 0.001 | |
| transScores | 0.001 | 0.000 | 0.001 | |
| vcf2sm | 0.111 | 0.004 | 0.118 | |