Last updated on 2025-07-27 08:48:30 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-gcc | 0.2.1 | 122.37 | 43.45 | 165.82 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.1 | 476.30 | OK | |||
| r-devel-windows-x86_64 | 0.2.1 | 173.00 | 146.00 | 319.00 | OK | |
| r-release-linux-x86_64 | 0.2.1 | 167.75 | 56.33 | 224.08 | ERROR | |
| r-release-macos-x86_64 | 0.2.1 | 145.00 | OK | |||
| r-release-windows-x86_64 | 0.2.1 | 153.00 | 146.00 | 299.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.1 | 148.00 | NOTE |
Version: 0.2.1
Check: examples
Result: ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.Marker
> ### Title: Conduct marker-level genetic association testing
> ### Aliases: GRAB.Marker
>
> ### ** Examples
>
> objNullFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB")
> load(objNullFile)
> class(obj.POLMM) # "POLMM_NULL_Model", that indicates an object from POLMM method.
[1] "POLMM_NULL_Model"
>
> OutputDir <- system.file("results", package = "GRAB")
> OutputFile <- paste0(OutputDir, "/simuOUTPUT.txt")
> GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
>
> ## make sure the output files does not exist at first
> if (file.exists(OutputFile)) file.remove(OutputFile)
> if (file.exists(paste0(OutputFile, ".index"))) file.remove(paste0(OutputFile, ".index"))
>
> GRAB.Marker(obj.POLMM,
+ GenoFile = GenoFile,
+ OutputFile = OutputFile
+ )
The below is the list of control parameters used in marker-level genetic association analysis.
2c("beta", "seBeta")mean0.150.00120100003
Reading bim file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim
Reading fam file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
setting PLINK object in CPP....
Reading bim file....
Reading fam file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
m_N: 1000
Setting position of samples in PLINK files....
posSampleInPlink: 501 510 600
SampleInModel: Subj-1 Subj-10 Subj-100
SampleInPlink: f1_1 f1_2 f1_3
Number of samples: 1000
Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data.
Number of all markers to test: 1100
Number of markers in each chunk: 10000
Number of chunks for all markers: 1
The current control$nMarkersEachChunk is 10000.
(2025-07-26 13:19:20.964078) ---- Analyzing Chunk 1/1: chrom 1 ----
Completed 0/1100 markers in the chunk.
Completed 1000/1100 markers in the chunk.
Warning in file(file, ifelse(append, "a", "w")) :
cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/results/simuOUTPUT.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Calls: GRAB.Marker -> writeOutputFile -> write.table -> file
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.1
Check: examples
Result: ERROR
Running examples in ‘GRAB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GRAB.Marker
> ### Title: Conduct marker-level genetic association testing
> ### Aliases: GRAB.Marker
>
> ### ** Examples
>
> objNullFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB")
> load(objNullFile)
> class(obj.POLMM) # "POLMM_NULL_Model", that indicates an object from POLMM method.
[1] "POLMM_NULL_Model"
>
> OutputDir <- system.file("results", package = "GRAB")
> OutputFile <- paste0(OutputDir, "/simuOUTPUT.txt")
> GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
>
> ## make sure the output files does not exist at first
> if (file.exists(OutputFile)) file.remove(OutputFile)
> if (file.exists(paste0(OutputFile, ".index"))) file.remove(paste0(OutputFile, ".index"))
>
> GRAB.Marker(obj.POLMM,
+ GenoFile = GenoFile,
+ OutputFile = OutputFile
+ )
The below is the list of control parameters used in marker-level genetic association analysis.
2c("beta", "seBeta")mean0.150.00120100003
Reading bim file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim
Reading fam file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
setting PLINK object in CPP....
Reading bim file....
Reading fam file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam
m_N: 1000
Setting position of samples in PLINK files....
posSampleInPlink: 501 510 600
SampleInModel: Subj-1 Subj-10 Subj-100
SampleInPlink: f1_1 f1_2 f1_3
Number of samples: 1000
Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data.
Number of all markers to test: 1100
Number of markers in each chunk: 10000
Number of chunks for all markers: 1
The current control$nMarkersEachChunk is 10000.
(2025-07-26 05:15:41.320504) ---- Analyzing Chunk 1/1: chrom 1 ----
Completed 0/1100 markers in the chunk.
Completed 1000/1100 markers in the chunk.
Warning in file(file, ifelse(append, "a", "w")) :
cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/GRAB/results/simuOUTPUT.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Calls: GRAB.Marker -> writeOutputFile -> write.table -> file
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.1
Check: installed package size
Result: NOTE
installed size is 18.1Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
libs 15.3Mb
Flavor: r-oldrel-macos-x86_64