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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MungeSumstats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MungeSumstats_1.7.16.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MungeSumstats.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MungeSumstats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MungeSumstats’ version ‘1.7.16’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MungeSumstats’ 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 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MungeSumstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: format_sumstats
> ### Title: Check that summary statistics from GWAS are in a homogeneous
> ###   format
> ### Aliases: format_sumstats
> 
> ### ** Examples
> 
> # Pass path to Educational Attainment Okbay sumstat file to a temp directory
> 
> eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt",
+     package = "MungeSumstats"
+ )
> 
> ## Call uses reference genome as default with more than 2GB of memory,
> ## which is more than what 32-bit Windows can handle so remove certain checks
> ## Using dbSNP = 144 for speed as it's smaller but you should use 155 unless
> ## you know what you are doing and need 144
> 
> is_32bit_windows <-
+     .Platform$OS.type == "windows" && .Platform$r_arch == "i386"
> if (!is_32bit_windows) {
+     reformatted <- format_sumstats(
+         path = eduAttainOkbayPth,
+         ref_genome = "GRCh37",
+         dbSNP = 144
+     )
+ } else {
+     reformatted <- format_sumstats(
+         path = eduAttainOkbayPth,
+         ref_genome = "GRCh37",
+         on_ref_genome = FALSE,
+         strand_ambig_filter = FALSE,
+         bi_allelic_filter = FALSE,
+         allele_flip_check = FALSE,
+         dbSNP=144
+     )
+ }


******::NOTE::******
 - Formatted results will be saved to `tempdir()` by default.
 - This means all formatted summary stats will be deleted upon ending the R session.
 - To keep formatted summary stats, change `save_path`  ( e.g. `save_path=file.path('./formatted',basename(path))` ),   or make sure to copy files elsewhere after processing  ( e.g. `file.copy(save_path, './formatted/' )`.
 ******************** 

Formatted summary statistics will be saved to ==>  /tmp/Rtmp7ralhJ/file37909188de98d.tsv.gz
Importing tabular file: /home/biocbuild/bbs-3.17-bioc/R/library/MungeSumstats/extdata/eduAttainOkbay.txt
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Ensuring all SNPs are on the reference genome.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 93 SNPs using BSgenome::snpsById...
Loading required package: BiocGenerics

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, 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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Killed
* 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:
     - 1 genome build(s)
  Collecting metadata from Open GWAS.
  Filtering metadata by substring criteria.
  Filtering metadata by sample/case/control/SNP size criteria.
  Excluding sample/case/control size with NAs.
  Found 3 GWAS datasets matching search criteria across:
     - 3 trait(s)
     - 1 population(s)
     - 2 category(ies)
     - 2 subcategory(ies)
     - 2 publication(s)
     - 2 consortia(ium)
     - 1 genome build(s)
  Collecting metadata from Open GWAS.
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MungeSumstats.Rmd’ using ‘UTF-8’... OK
  ‘OpenGWAS.Rmd’ using ‘UTF-8’... OK
  ‘docker.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MungeSumstats.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MungeSumstats
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘MungeSumstats’ ...
** 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 (MungeSumstats)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(MungeSumstats)
> 
> test_check("MungeSumstats")
Collecting metadata from Open GWAS.
Filtering metadata by substring criteria.
Found 3 GWAS datasets matching search criteria across:
   - 3 trait(s)
   - 1 population(s)
   - 2 category(ies)
   - 2 subcategory(ies)
   - 2 publication(s)
   - 2 consortia(ium)
   - 1 genome build(s)
Collecting metadata from Open GWAS.
Filtering metadata by substring criteria.
Filtering metadata by sample/case/control/SNP size criteria.
Excluding sample/case/control size with NAs.
Found 3 GWAS datasets matching search criteria across:
   - 3 trait(s)
   - 1 population(s)
   - 2 category(ies)
   - 2 subcategory(ies)
   - 2 publication(s)
   - 2 consortia(ium)
   - 1 genome build(s)
Collecting metadata from Open GWAS.
Killed