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 13:40:02 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLstats_1.10.1.tar.gz |
| StartedAt: 2018-04-12 04:44:26 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 04:56:20 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 713.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gQTLstats.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gQTLstats_1.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gQTLstats’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 65.9Mb
sub-directories of 1Mb or more:
data 11.0Mb
doc 1.5Mb
registries 18.8Mb
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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clipPCs 39.053 0.941 40.679
cisAssoc 23.501 1.055 25.075
gQTLs 9.477 0.945 10.665
eqBox2 7.885 0.259 8.265
queryVCF 7.856 0.222 8.224
manhWngr 4.761 0.138 5.004
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.
gQTLstats.Rcheck/00install.out
* installing *source* package ‘gQTLstats’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (gQTLstats)
gQTLstats.Rcheck/tests/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-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.
> 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: /Library/Frameworks/R.framework/Versions/3.4/Resources/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 04:56:15 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
254.003 11.588 271.385
gQTLstats.Rcheck/gQTLstats-Ex.timings
| name | user | system | elapsed | |
| FDRsupp-class | 0.002 | 0.000 | 0.002 | |
| TransStore-class | 0.001 | 0.000 | 0.001 | |
| TransStore | 0.000 | 0.000 | 0.001 | |
| cisAssoc | 23.501 | 1.055 | 25.075 | |
| clipPCs | 39.053 | 0.941 | 40.679 | |
| directPlot | 0.025 | 0.001 | 0.026 | |
| enumerateByFDR | 0.001 | 0.001 | 0.001 | |
| eqBox2 | 7.885 | 0.259 | 8.265 | |
| filtFDR | 0.020 | 0.001 | 0.021 | |
| gQTLs | 9.477 | 0.945 | 10.665 | |
| hmm878 | 0.966 | 0.062 | 1.047 | |
| manhWngr | 4.761 | 0.138 | 5.004 | |
| mixedVCFtoSnpMatrix | 0.584 | 0.016 | 0.615 | |
| pifdr | 1.578 | 0.081 | 1.697 | |
| qqStore | 0.001 | 0.000 | 0.000 | |
| queryVCF | 7.856 | 0.222 | 8.224 | |
| senstab | 2.693 | 0.024 | 2.758 | |
| setFDRfunc | 0.045 | 0.001 | 0.048 | |
| storeToStats | 0.001 | 0.000 | 0.001 | |
| tqbrowser | 0.015 | 0.000 | 0.016 | |
| transAssoc | 0.001 | 0.001 | 0.001 | |
| transBrowse | 0.001 | 0.000 | 0.001 | |
| tsByRank | 0.002 | 0.000 | 0.003 | |
| txsPlot | 0.020 | 0.002 | 0.022 | |