Issues with BITE and GENabel dependancy of R script

[kcairns]

Hi there, do you have a work around for the R package BITE and it's dependancy on GENABEL? BITE is used in your R scripts so I was hoping you would have some tips on how to install it. I've tried multiple times to install BITE after updating my R version and now the Genabel install fails during compilation. I'm on a mac if that helps.

This is the exact error I get:

clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DCOMPILE_WITH_R -fPIC  -Wall -g -O2  -c dometa.cpp -o dometa.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DCOMPILE_WITH_R -fPIC  -Wall -g -O2  -c export_plink.cpp -o export_plink.o
export_plink.cpp:116:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
            fileWoA << " " << Genotype[gtMatrix[i][csnp]];
                                      ^~~~~~~~~~~~~~~~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fexact.c -o fexact.o
fexact.c:1025:6: error: use of undeclared identifier 'PROBLEM'
            PROBLEM "Bug in FEXACT: gave negative key" RECOVER(NULL_ENTRY);
            ^
fexact.c:1806:5: error: use of undeclared identifier 'PROBLEM'
    PROBLEM "FEXACT error %d.\n%s", icode, mes RECOVER(NULL_ENTRY);
    ^
2 errors generated.
make: *** [fexact.o] Error 1
ERROR: compilation failed for package ‘GenABEL’
* removing ‘/Users/kyliecairns/Library/R/x86_64/4.2/library/GenABEL’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/y7/rpt5qcnj4ggf_dxzfd_646z80000gn/T//RtmpAabixH/filebd3d1ba0b70/GenABEL_1.8-0.tar.gz’ had non-zero exit status

[WickEmm]

Dear Carolin and Kcairns, I have the same problem : have tried multiple times to install GenABEL and BITE, with no success (I use R 4.2.2 for Windows). And no solution from the BITE package developer, nor from people who already published results mentioning the R BITE...I would like to visualize the Treemix results without having to use this package, do you have alternative solutions please ? Best,

[kcairns]

I don’t – I’ve decided to install an old version of R with GenABEL and BITE to visualise the Treemix results.

Kylie

From: WickEmm @.> Date: Friday, 17 March 2023 at 3:25 am To: carolindahms/TreeMix @.> Cc: Kylie Cairns @.>, Author @.> Subject: Re: [carolindahms/TreeMix] Issues with BITE and GENabel dependancy of R script (Issue #3)

Dear Carolin and Kcairns, I have the same problem : have tried multiple times to install GenABEL and BITE, with no success (I use R 4.2.2 for Windows). And no solution from the BITE package developer, nor from people who already published results mentioning the R BITE...I would like to visualize the Treemix results without having to use this package, do you have alternative solutions please ? Best,

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[WickEmm]

Dear Kylie, Thanks for your quick reply. Can you precise me which version of R you succeeded with? I tried with version 3.5.0 and 3.6 and still failed to install this nasty packages. Thanks in advance for your help,

[PeterResutik]

Hi all, I had the same issue so I tested several R versions. Eventually, it did work for the version 4.1.3. Hope this helps. Best