- using R Under development (unstable) (2026-06-06 r90114)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-16 (Debian 16.1.0-1) 16.1.0
GNU Fortran (Debian 16.1.0-1) 16.1.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-06-07 10:57:53 UTC
- checking for file ‘GRAB/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘GRAB’ version ‘0.2.4’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [2s/3s] OK
- checking package namespace information ... OK
- checking package dependencies ... INFO
Package suggested but not available for checking: ‘dbplyr’
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- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘GRAB’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-16 (Debian 16.1.0-1) 16.1.0’
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking DESCRIPTION meta-information ... OK
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- checking for left-over files ... OK
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- 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 ... [1s/1s] OK
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- checking loading without being on the library search path ... [1s/1s] OK
- checking use of S3 registration ... 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 ... [12s/15s] OK
- checking Rd files ... [0s/1s] OK
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- checking for unstated dependencies in examples ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
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- checking compiled code ... OK
- checking examples ... [5s/6s] ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.ReadGeno
> ### Title: Read genotype data from multiple file formats
> ### Aliases: GRAB.ReadGeno
>
> ### ** Examples
>
> ## Raw genotype data
> RawFile <- system.file("extdata", "simuRAW.raw.gz", package = "GRAB")
> GenoMat <- data.table::fread(RawFile)
> GenoMat[1:10, 1:10]
FID IID PAT MAT SEX PHENOTYPE SNP_1_A SNP_2_A SNP_3_A SNP_4_A
<char> <char> <int> <int> <int> <int> <int> <int> <int> <int>
1: f1_1 f1_1 0 0 1 -9 0 1 2 2
2: f1_2 f1_2 0 0 1 -9 1 1 1 0
3: f1_3 f1_3 0 0 1 -9 1 1 0 1
4: f1_4 f1_4 0 0 1 -9 1 1 1 2
5: f1_5 f1_5 0 0 1 -9 0 2 2 1
6: f1_6 f1_6 0 0 1 -9 0 NA 2 1
7: f1_7 f1_7 0 0 1 -9 0 1 1 1
8: f1_8 f1_8 0 0 1 -9 1 1 1 1
9: f1_9 f1_9 0 0 1 -9 1 1 2 1
10: f1_10 f1_10 0 0 1 -9 1 2 1 2
>
> ## PLINK files
> PLINKFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
> # If include/exclude files are not specified, then control$AllMarker should be TRUE
> GenoList <- GRAB.ReadGeno(PLINKFile, control = list(AllMarkers = TRUE))
[INFO] 2026-06-07 12:58:46 Marker selection: Analyzing all markers in the genotype file.
[INFO] 2026-06-07 12:58:46 Reading bim file: simuPLINK.bim
[INFO] 2026-06-07 12:58:46 Reading fam file: simuPLINK.fam
[INFO] 2026-06-07 12:58:46 Using all samples from genotype file (1000 samples)
[INFO] 2026-06-07 12:58:46 Setting up PLINK object in C++ ...
Number of subjects with genotype: 1000
[INFO] 2026-06-07 12:58:46 Reading genotypes: 1000 subjects, 1100 markers
[INFO] 2026-06-07 12:58:46 Genotype reading completed
> GenoMat <- GenoList$GenoMat
> markerInfo <- GenoList$markerInfo
> head(GenoMat[, 1:6])
SNP_1 SNP_2 SNP_3 SNP_4 SNP_5 SNP_6
f1_1 0 1 2 2 1 0
f1_2 1 1 1 0 0 0
f1_3 1 1 0 1 0 NaN
f1_4 1 1 1 2 1 0
f1_5 0 2 2 1 NaN 0
f1_6 0 NaN 2 1 0 0
> head(markerInfo)
CHROM POS ID REF ALT
1 1 1 SNP_1 G A
2 1 2 SNP_2 G A
3 1 3 SNP_3 G A
4 1 4 SNP_4 G A
5 1 5 SNP_5 G A
6 1 6 SNP_6 G A
>
> ## BGEN files (Note the different REF/ALT order for BGEN and PLINK formats)
> BGENFile <- system.file("extdata", "simuBGEN.bgen", package = "GRAB")
> GenoList <- GRAB.ReadGeno(BGENFile, control = list(AllMarkers = TRUE))
[INFO] 2026-06-07 12:58:46 Marker selection: Analyzing all markers in the genotype file.
[INFO] 2026-06-07 12:58:46 Reading sample file: simuBGEN.sample
[INFO] 2026-06-07 12:58:46 Reading bgi file: simuBGEN.bgen.bgi
Error in check_dbplyr() :
The package "dbplyr" is required to communicate with database backends.
Calls: GRAB.ReadGeno ... tbl.DBIConnection -> check_dbplyr -> check_installed
Execution halted
- checking PDF version of manual ... [4s/5s] OK
- checking HTML version of manual ... [3s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR