problem with GenABEL repository with Mac M1 pro

[marcoabbestia]

Dear all, I'm trying to install BITE on mac M1 pro but I'm having trouble installing the genABEL dependency, the following message appears:

export_plink.cpp:116:39: warning: array subscript is of type 'char' [-Wchar-subscripts] fileWoA << " " << Genotype[gtMatrix[i][csnp]]; ^~~~~~ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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 ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/GenABEL’

Is there any way to fix the problem? Thank you

Marco

[capemaster]

Dear Marco, thank you for pointing it out. I have good news for you concerning BITE: we are working to eliminate the obsolete dependencies but you will have to be patient for the next version of the package.

At the moment, i can only suggest you to try with another platform. The error seems to be connected to the C compiler and we are not able to provide support in this. Maybe trying to install via homebrew a different version of the compiler? Sorry for not being able to help.

[marcoabbestia]

Dear Stefano, thank you very much for you answer. I was thinking of setting up a virtual machine to emulate a different type of chip architecture in my MacBook M1. What do you think? I'm happy to know that a new version of BITE will be ready, it's a very nice package. ciao Marco

[capemaster]

Yes I think this might work. I am currently have bite in this environment:

> print(sessionInfo()) R version 4.0.5 (2021-03-31) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Stream 8 Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BITE_1.2.0008 beanplot_1.2 kableExtra_1.3.4 knitr_1.33 rmarkdown_2.7 car_3.0-10 [7] carData_3.0-4 GenABEL_1.8-0 GenABEL.data_1.0.0 MASS_7.3-53.1 RColorBrewer_1.1-2 reshape2_1.4.4 [13] RCircos_1.1.3 loaded via a namespace (and not attached): [1] zip_2.1.1 Rcpp_1.0.7 compiler_4.0.5 pillar_1.6.0 cellranger_1.1.0 plyr_1.8.6 [7] forcats_0.5.1 tools_4.0.5 digest_0.6.27 viridisLite_0.4.0 evaluate_0.14 lifecycle_1.0.0 [13] tibble_3.1.1 pkgconfig_2.0.3 rlang_0.4.10 openxlsx_4.2.3 rstudioapi_0.13 curl_4.3 [19] haven_2.4.1 xfun_0.22 rio_0.5.26 xml2_1.3.2 httr_1.4.2 stringr_1.4.0 [25] systemfonts_1.0.1 vctrs_0.3.7 hms_1.0.0 webshot_0.5.2 svglite_2.0.0 glue_1.4.2 [31] data.table_1.14.0 R6_2.5.0 fansi_0.4.2 readxl_1.3.1 foreign_0.8-81 magrittr_2.0.1 [37] scales_1.1.1 ellipsis_0.3.1 htmltools_0.5.1.1 rvest_1.0.0 abind_1.4-5 colorspace_2.0-0 [43] utf8_1.2.1 stringi_1.5.3 munsell_0.5.0 crayon_1.4.1

[marcoabbestia]

ok I will try it! greetings

Il giorno mar 14 mar 2023 alle ore 10:52 capemaster < @.***> ha scritto:

Yes I think this might work. I am currently have bite in this environment: CentOS 8

`

print(sessionInfo()) R version 4.0.5 (2021-03-31) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Stream 8

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BITE_1.2.0008 beanplot_1.2 kableExtra_1.3.4 knitr_1.33 rmarkdown_2.7 car_3.0-10 [7] carData_3.0-4 GenABEL_1.8-0 GenABEL.data_1.0.0 MASS_7.3-53.1 RColorBrewer_1.1-2 reshape2_1.4.4 [13] RCircos_1.1.3

loaded via a namespace (and not attached): [1] zip_2.1.1 Rcpp_1.0.7 compiler_4.0.5 pillar_1.6.0 cellranger_1.1.0 plyr_1.8.6 [7] forcats_0.5.1 tools_4.0.5 digest_0.6.27 viridisLite_0.4.0 evaluate_0.14 lifecycle_1.0.0 [13] tibble_3.1.1 pkgconfig_2.0.3 rlang_0.4.10 openxlsx_4.2.3 rstudioapi_0.13 curl_4.3 [19] haven_2.4.1 xfun_0.22 rio_0.5.26 xml2_1.3.2 httr_1.4.2 stringr_1.4.0 [25] systemfonts_1.0.1 vctrs_0.3.7 hms_1.0.0 webshot_0.5.2 svglite_2.0.0 glue_1.4.2 [31] data.table_1.14.0 R6_2.5.0 fansi_0.4.2 readxl_1.3.1 foreign_0.8-81 magrittr_2.0.1 [37] scales_1.1.1 ellipsis_0.3.1 htmltools_0.5.1.1 rvest_1.0.0 abind_1.4-5 colorspace_2.0-0 [43] utf8_1.2.1 stringi_1.5.3 munsell_0.5.0 crayon_1.4.1 `

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[hai-dee]

Any update on when the GenABEL dependency will be removed from BITE?

[capemaster]

Hi, indeed we have. BITE 2 is now available in the downloads. The package have been substantially rewritten!

Have fun!!!