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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scQTLtools.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings scQTLtools_0.99.11.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/scQTLtools.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scQTLtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scQTLtools' version '0.99.11'
* package encoding: UTF-8
* 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 'scQTLtools' can be installed ... OK
* checking installed package size ... OK
* 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 code 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 ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'scQTLtools-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: callQTL
> ### Title: callQTL: Uncover single-cell eQTLs exclusively using scRNA-seq
> ###   data. A function designed to identify eQTLs from scRNA-seq data.
> ### Aliases: callQTL
> 
> ### ** Examples
> 
> data(testEQTL)
> library(biomaRt)
> gene_mart <- useEnsembl(biomart = "genes",
+                         dataset = "hsapiens_gene_ensembl",
+                         mirror = 'asia')
Ensembl site unresponsive, trying www mirror
Ensembl site unresponsive, trying useast mirror
Error in .chooseEnsemblMirror(mirror = mirror, http_config = http_config) : 
  Unable to query any Ensembl site
Calls: useEnsembl -> .chooseEnsemblMirror
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DESeq_normalize 10.61   0.45   11.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-callQTL.R:42:3'): Function handles upstream/downstream parameters correctly ──
  Error in `.chooseEnsemblMirror(mirror = mirror, http_config = http_config)`: Unable to query any Ensembl site
  Backtrace:
      ▆
   1. └─scQTLtools::callQTL(eqtl, downstream = -8.5e+07, upstream = 2e+07) at test-callQTL.R:42:3
   2.   └─scQTLtools:::match_gene_snp(...)
   3.     └─scQTLtools::createGeneLoc(geneList, gene_mart, geneDataset, OrgDb)
   4.       └─biomaRt::useEnsembl(biomart = "genes", dataset = geneDataset)
   5.         └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, http_config = http_config)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 52 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/scQTLtools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL scQTLtools
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'scQTLtools' ...
** this is package 'scQTLtools' version '0.99.11'
** 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 (scQTLtools)

R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(scQTLtools)

> 
> test_check("scQTLtools")
Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
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")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

No Normalized counts found named 'normcounts',
                you can achieve data normalization with `normalizeGene()`,
                or check if it is has been renamed.
Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705


Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Normalization completed using method: CPM

Dimensions of normalized data:84 2705

Normalization completed using method: TPM

Dimensions of normalized data:84 2705

converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Normalization completed using method: DESeq

Dimensions of normalized data:84 2705

Normalization completed using method: limma

Dimensions of normalized data:84 2705

Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Normalization completed using method: logNormalize

Dimensions of normalized data:84 2705

Start the sc-eQTLs calling.
Matrix:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
Normalization completed using method: logNormalize

Dimensions of normalized data:74 500

Start the sc-eQTLs calling.
CMP:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
GMP:
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
Finished!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 52 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-callQTL.R:42:3'): Function handles upstream/downstream parameters correctly ──
Error in `.chooseEnsemblMirror(mirror = mirror, http_config = http_config)`: Unable to query any Ensembl site
Backtrace:
    ▆
 1. └─scQTLtools::callQTL(eqtl, downstream = -8.5e+07, upstream = 2e+07) at test-callQTL.R:42:3
 2.   └─scQTLtools:::match_gene_snp(...)
 3.     └─scQTLtools::createGeneLoc(geneList, gene_mart, geneDataset, OrgDb)
 4.       └─biomaRt::useEnsembl(biomart = "genes", dataset = geneDataset)
 5.         └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, http_config = http_config)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 52 ]
Error: Test failures
Execution halted