Closed marcoabbestia closed 1 year ago
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.
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
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
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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Any update on when the GenABEL dependency will be removed from BITE?
Hi, indeed we have. BITE 2 is now available in the downloads. The package have been substantially rewritten!
Have fun!!!
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’Is there any way to fix the problem? Thank you
Marco