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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:MungeSumstats.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings MungeSumstats_1.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MungeSumstats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MungeSumstats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MungeSumstats’ version ‘1.10.1’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ==>  /home/biocbuild/tmp/RtmpsNIurT/file1a967a112d71d8.tsv.gz
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
Importing tabular file: /home/biocbuild/R/R-4.3.1/site-library/MungeSumstats/extdata/eduAttainOkbay.txt
Checking for empty columns.
Infer Effect Column
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Allele columns are ambiguous, attempting to infer direction
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 93 SNPs using BSgenome::snpsById...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1745512 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     - 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
  Checking for incorrect base-pair positions
  Checking for correct direction of A1 (reference) and A2 (alternative allele).
  Loading SNPlocs data.
  Loading reference genome data.
  Preprocessing RSIDs.
  Validating RSIDs of 93 SNPs using BSgenome::snpsById...
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MungeSumstats.Rcheck/00check.log’
for details.