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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:gQTLstats.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings gQTLstats_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/gQTLstats.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gQTLstats/DESCRIPTION’ ... OK
* this is package ‘gQTLstats’ version ‘1.20.0’
* 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 64.8Mb
  sub-directories of 1Mb or more:
    data        11.0Mb
    registries  18.9Mb
    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 ... OK
* 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’
gmod2: no visible binding for global variable ‘exonsBy’
gmod2: no visible global function definition for ‘TxDb’
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 : 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’
boxswarm,SnpToGeneQTL: no visible binding for global variable ‘g1’
Undefined global functions or variables:
  DNAStringSetList MAF TabixFile TxDb assoc calls ch chisq criterion ex
  exonsBy experiments g1 geom_boxplot gt i id maf mindist ml10fdr nth
  permScore_1 permScore_2 permScore_3 probeid 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 ... NOTE
Output for data("bigfiltFDR", package = "gQTLstats"):
  
  
Output for data("bigrawFDR", package = "gQTLstats"):
  
  
Output for data("filtFDR", package = "gQTLstats"):
  
  
Output for data("rawFDR", package = "gQTLstats"):
  
  
Output for data("sensByProbe", package = "gQTLstats"):
  
  
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
clipPCs  42.883  0.852  43.745
cisAssoc 25.917  0.436  27.327
queryVCF 10.767  0.104  10.892
gQTLs     9.992  0.144  10.451
eqBox2    9.179  0.108   9.292
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/gQTLstats.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL gQTLstats
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘gQTLstats’ ...
** 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 (gQTLstats)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> BiocGenerics:::testPackage("gQTLstats")

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



Loading required package: geuvPack
Loading required package: SummarizedExperiment
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 objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

clipping PCs 1,2 from exprs
[W::bcf_hdr_check_sanity] GL should be declared as Number=G

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 following object is masked from 'package:base':

    isFALSE

The development of BatchJobs and BatchExperiments is discontinued.
Consider switching to 'batchtools' for new features and improved stability
Sourced 1 configuration files: 
  1: /home/biocbuild/bbs-3.11-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 -- Sat Oct 17 02:15:21 2020 
*********************************************** 
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 
288.512   3.157 294.848