VJ Carey
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/gQTLstats |
| Branch: RELEASE_3_6 |
| Last Commit: 070d681 |
| Last Changed Date: 2017-12-03 13:09:47 -0400 (Sun, 03 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:25:29 -0400 (Thu, 12 Apr 2018).
| Package 611/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gQTLstats 1.10.1 VJ Carey
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: gQTLstats |
| Version: 1.10.1 |
| Command: rm -rf gQTLstats.buildbin-libdir gQTLstats.Rcheck && mkdir gQTLstats.buildbin-libdir gQTLstats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLstats.buildbin-libdir gQTLstats_1.10.1.tar.gz >gQTLstats.Rcheck\00install.out 2>&1 && cp gQTLstats.Rcheck\00install.out gQTLstats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gQTLstats.buildbin-libdir --install="check:gQTLstats-install.out" --force-multiarch --no-vignettes --timings gQTLstats_1.10.1.tar.gz |
| StartedAt: 2018-04-12 00:31:26 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:51:21 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 1195.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gQTLstats.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf gQTLstats.buildbin-libdir gQTLstats.Rcheck && mkdir gQTLstats.buildbin-libdir gQTLstats.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLstats.buildbin-libdir gQTLstats_1.10.1.tar.gz >gQTLstats.Rcheck\00install.out 2>&1 && cp gQTLstats.Rcheck\00install.out gQTLstats-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gQTLstats.buildbin-libdir --install="check:gQTLstats-install.out" --force-multiarch --no-vignettes --timings gQTLstats_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gQTLstats/DESCRIPTION' ... OK
* this is package 'gQTLstats' version '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'gQTLstats' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/TransStore-class.Rd:19: missing file link 'Registry'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/TransStore.Rd:18: missing file link 'Registry'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:37: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:40: missing file link 'TabixFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:63: missing file link 'col.summary'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:75: missing file link 'isSNV'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/clipPCs.Rd:24: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/clipPCs.Rd:50: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/eqBox2.Rd:27: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/gQTLs.Rd:29: missing file link 'readVcf'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/manhWngr.Rd:28: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:18: missing file link 'CollapsedVCF-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:24: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:32: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:50: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/qqStore.Rd:28: missing file link 'storeToQuantiles'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/queryVCF.Rd:29: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/tsByRank.Rd:52: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 64.9Mb
sub-directories of 1Mb or more:
data 11.0Mb
registries 18.5Mb
vcf 33.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'Homo.sapiens' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'ldblock'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TransStore: no visible binding for global variable 'i'
TransStore : <anonymous>: no visible binding for global variable 'i'
cisAssoc: no visible global function definition for 'DNAStringSetList'
cisCount: no visible global function definition for 'DNAStringSetList'
cisEsts: no visible global function definition for 'DNAStringSetList'
eqBox4: no visible binding for global variable 'gt'
eqBox4: no visible binding for global variable 'ex'
eqBox4: no visible binding for global variable 'id'
eqBox4: no visible global function definition for 'geom_boxplot'
gQTLs: no visible binding for global variable 'ch'
gQTLs: no visible global function definition for 'path'
gmod2: no visible binding for global variable 'exonsBy'
gmod2: no visible binding for global variable 'Homo.sapiens'
manhWngr: no visible binding for global variable 'ml10fdr'
maxByFeature: no visible binding for global variable 'snp'
maxByFeature: no visible binding for global variable 'chisq'
maxByFeature: no visible binding for global variable 'probeid'
maxByProbeOLD: no visible binding for global variable 'snp'
maxByProbeOLD: no visible binding for global variable 'probeid'
maxByProbeOLD: no visible binding for global variable 'chisq'
maxByProbeOLD: no visible binding for global variable 'permScore_1'
maxByProbeOLD: no visible binding for global variable 'permScore_2'
maxByProbeOLD: no visible binding for global variable 'permScore_3'
plot.senstab: no visible binding for global variable 'MAF'
plot.senstab: no visible binding for global variable 'value'
plot.senstab: no visible binding for global variable 'criterion'
plot.table.sensobj: no visible binding for global variable 'maf'
plot.table.sensobj: no visible binding for global variable 'calls'
prep.cisAssocNB: no visible global function definition for
'DNAStringSetList'
setFDRfunc: no visible binding for global variable 'assoc'
storeToHist: no visible binding for global variable 'x'
storeToMaxAssocBySNP: no visible binding for global variable 'snp'
storeToMaxAssocBySNP: no visible binding for global variable 'chisq'
storeToMaxAssocBySNP: no visible binding for global variable
'permScore_1'
storeToMaxAssocBySNP: no visible binding for global variable
'permScore_2'
storeToMaxAssocBySNP: no visible binding for global variable
'permScore_3'
storeToMaxAssocBySNP: no visible global function definition for 'nth'
storeToMaxAssocBySNP: no visible binding for global variable 'MAF'
storeToMaxAssocBySNP: no visible binding for global variable 'probeid'
storeToMaxAssocBySNP: no visible binding for global variable 'mindist'
tqbrowser: no visible global function definition for 'experiments'
tqbrowser: no visible global function definition for 'plotlyOutput'
tqbrowser : server: no visible global function definition for
'renderPlotly'
tqbrowser : server: no visible global function definition for 'path'
tqbrowser : server: no visible global function definition for
'experiments'
tqbrowser : server: no visible global function definition for
'TabixFile'
tqbrowser : server: no visible binding for global variable 'assoc'
tqbrowser : server: no visible binding for global variable 'stateid'
tqbrowser : server: no visible binding for global variable 'state'
transTable: no visible binding for global variable 'i'
tsByRank_sing: no visible binding for global variable 'i'
tsByRank_sing : <anonymous>: no visible binding for global variable 'i'
vecsToFDR: possible error in vecToHist(permvec, getter = getter, breaks
= c(0, xq, 1e+10), filter = filter, ids = ids): unused arguments
(getter = getter, ids = ids)
vecsToFDR: no visible binding for global variable 'nperm'
boxswarm,SnpToGeneQTL: no visible binding for global variable 'g1'
Undefined global functions or variables:
DNAStringSetList Homo.sapiens MAF TabixFile assoc calls ch chisq
criterion ex exonsBy experiments g1 geom_boxplot gt i id maf mindist
ml10fdr nperm nth path permScore_1 permScore_2 permScore_3
plotlyOutput probeid renderPlotly snp state stateid value x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 8 marked Latin-1 strings
Note: found 12 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipPCs 56.94 1.44 58.37
cisAssoc 22.96 0.92 25.17
gQTLs 13.09 1.23 14.33
eqBox2 11.77 0.31 12.08
queryVCF 10.62 0.22 10.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipPCs 32.18 1.22 33.39
cisAssoc 25.01 0.95 25.97
gQTLs 10.19 1.85 12.03
eqBox2 8.90 0.34 9.25
queryVCF 8.50 0.15 8.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.R'
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
'TxDb.Hsapiens.UCSC.hg19.knownGene' 'org.Hs.eg.db'
* 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: 1 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck/00check.log'
for details.
gQTLstats.Rcheck/00install.out
install for i386
* installing *source* package 'gQTLstats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'gQTLstats'
finding HTML links ... done
FDRsupp-class html
TransStore-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/TransStore-class.Rd:19: missing file link 'Registry'
TransStore html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/TransStore.Rd:18: missing file link 'Registry'
cisAssoc html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:37: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:40: missing file link 'TabixFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:63: missing file link 'col.summary'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/cisAssoc.Rd:75: missing file link 'isSNV'
clipPCs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/clipPCs.Rd:24: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/clipPCs.Rd:50: missing file link 'RangedSummarizedExperiment'
directPlot html
enumerateByFDR html
finding level-2 HTML links ... done
eqBox2 html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/eqBox2.Rd:27: missing file link 'RangedSummarizedExperiment'
filtFDR html
gQTLs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/gQTLs.Rd:29: missing file link 'readVcf'
gQTLstats-package html
hmm878 html
manhWngr html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/manhWngr.Rd:28: missing file link 'GRanges'
mixedVCFtoSnpMatrix html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:18: missing file link 'CollapsedVCF-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:24: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:32: missing file link 'genotypeToSnpMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:50: missing file link 'genotypeToSnpMatrix'
pifdr html
qqStore html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/qqStore.Rd:28: missing file link 'storeToQuantiles'
queryVCF html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/queryVCF.Rd:29: missing file link 'genotypeToSnpMatrix'
senstab html
setFDRfunc html
storeToStats html
tqbrowser html
transAssoc html
transBrowse html
tsByRank html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpak80BQ/R.INSTALL20ec78a77ce7/gQTLstats/man/tsByRank.Rd:52: missing file link 'GRanges'
txsPlot html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'gQTLstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLstats' as gQTLstats_1.10.1.zip
* DONE (gQTLstats)
In R CMD INSTALL
In R CMD INSTALL
|
gQTLstats.Rcheck/tests_i386/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage("gQTLstats")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: geuvPack
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
clipping PCs 1,2 from exprs
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
Loading required package: geuvStore2
Loading required package: BatchJobs
Loading required package: BBmisc
Attaching package: 'BBmisc'
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:BiocGenerics':
normalize
The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files:
1: C:/Users/biocbuild/bbs-3.6-bioc/R/library/BatchJobs/etc/BatchJobs_global_config.R
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
measure.mem: TRUE
Loading required package: gQTLBase
NOTE: there were 41 samples not found (of 462 requested).
using assay() to extract 'expression' matrix from RangedSummarizedExperiment
counting tests...
counting #NA...
obtaining assoc quantiles...
computing perm_assoc histogram....
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
RUNIT TEST PROTOCOL -- Thu Apr 12 00:46:52 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gQTLstats RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(x, ...) : non-diploid variants are set to NA
2: In col.summary(gtdata[[1]]) :
69 rows were empty - ignored when calculating call rates
3: In .local(x, ...) : non-diploid variants are set to NA
4: In col.summary(gtdata$genotypes) :
69 rows were empty - ignored when calculating call rates
5: executing %dopar% sequentially: no parallel backend registered
6: In .local(x, ...) : non-diploid variants are set to NA
7: In .local(x, ...) : non-diploid variants are set to NA
8: In col.summary(gtdata[[1]]) :
238 rows were empty - ignored when calculating call rates
9: In .local(x, ...) : non-diploid variants are set to NA
10: In col.summary(gtdata$genotypes) :
238 rows were empty - ignored when calculating call rates
>
> proc.time()
user system elapsed
255.93 9.90 267.54
|
gQTLstats.Rcheck/tests_x64/test-all.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-w64-mingw32/x64 (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.
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> BiocGenerics:::testPackage("gQTLstats")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: geuvPack
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
clipping PCs 1,2 from exprs
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
Loading required package: geuvStore2
Loading required package: BatchJobs
Loading required package: BBmisc
Attaching package: 'BBmisc'
The following object is masked from 'package:Biostrings':
collapse
The following object is masked from 'package:IRanges':
collapse
The following object is masked from 'package:BiocGenerics':
normalize
The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files:
1: C:/Users/biocbuild/bbs-3.6-bioc/R/library/BatchJobs/etc/BatchJobs_global_config.R
BatchJobs configuration:
cluster functions: Interactive
mail.from:
mail.to:
mail.start: none
mail.done: none
mail.error: none
default.resources:
debug: FALSE
raise.warnings: FALSE
staged.queries: TRUE
max.concurrent.jobs: Inf
fs.timeout: NA
measure.mem: TRUE
Loading required package: gQTLBase
NOTE: there were 41 samples not found (of 462 requested).
using assay() to extract 'expression' matrix from RangedSummarizedExperiment
counting tests...
counting #NA...
obtaining assoc quantiles...
computing perm_assoc histogram....
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
checking for universal heterozygous loci for exclusion (as dropUnivHet == TRUE) ...
done checking.
RUNIT TEST PROTOCOL -- Thu Apr 12 00:51:16 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gQTLstats RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(x, ...) : non-diploid variants are set to NA
2: In col.summary(gtdata[[1]]) :
69 rows were empty - ignored when calculating call rates
3: In .local(x, ...) : non-diploid variants are set to NA
4: In col.summary(gtdata$genotypes) :
69 rows were empty - ignored when calculating call rates
5: executing %dopar% sequentially: no parallel backend registered
6: In .local(x, ...) : non-diploid variants are set to NA
7: In .local(x, ...) : non-diploid variants are set to NA
8: In col.summary(gtdata[[1]]) :
238 rows were empty - ignored when calculating call rates
9: In .local(x, ...) : non-diploid variants are set to NA
10: In col.summary(gtdata$genotypes) :
238 rows were empty - ignored when calculating call rates
>
> proc.time()
user system elapsed
247.46 5.60 262.85
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gQTLstats.Rcheck/examples_i386/gQTLstats-Ex.timings
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gQTLstats.Rcheck/examples_x64/gQTLstats-Ex.timings
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