Hi Bowen, I believe there might be an issue with the Mac ARM64 binary for preprocessCore, which is where the error is coming from in the support issue you mentioned. I am going to trigger a rebuild of the binaries, which may not be available until this weekend. I can follow up when the new binaries are built so you can try installing affy via BiocManager. Thanks for your patience and also bring this up.
Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team ________________________________ From: R-SIG-Mac <r-sig-mac-boun...@r-project.org> on behalf of Ken Beath <k...@kjbeath.com.au> Sent: Tuesday, December 13, 2022 5:27 AM To: Bowen Lai <bwlaisp...@163.com> Cc: r-sig-mac@r-project.org <r-sig-mac@r-project.org> Subject: Re: [R-SIG-Mac] Unable to library package "affy" ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** The question is why do you need to install from sources. Using a standard R install and then following the instructions at https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_install_&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=gMuHajvpZe3IR5u1PjVWd7QfLsJ0e8G-XnVqwDn9OaFkN8mSzr_84YXGXJ8kbAkP&s=i-7EuLULoifrPUaLsw3dstDjYcM8iWjyyqELdRCdJPw&e= and then use BiocManager::install(�affy�) It works for me. If it doesn�t for you, then you have done something to your installation. Life will be easier if you just use a standard installation. Ken > On 13 Dec 2022, at 4:18 pm, Bowen Lai <bwlaisp...@163.com> wrote: > > R version: 4.2.2 > Arm64 with M1 SoC > > > my problem is totally same as this guy > https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_9148182_&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=gMuHajvpZe3IR5u1PjVWd7QfLsJ0e8G-XnVqwDn9OaFkN8mSzr_84YXGXJ8kbAkP&s=0r7gVO2_08JIA_969oP0NBI--EPp7mL5sjSyy9BL_wk&e= > so i search in Google and downlaod gfortan is neccessary. > Therefore, I have download ARM64 Macs: > gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz from > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_R-2Dmacos_gcc-2Ddarwin-2Darm64_releases_tag_R-2D4.2.0-2Drelease&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=gMuHajvpZe3IR5u1PjVWd7QfLsJ0e8G-XnVqwDn9OaFkN8mSzr_84YXGXJ8kbAkP&s=pygYxF3QudgsgdTQncb6Xr5_G2lhm0x9fAqCHDrKAPc&e= > , but i can't understand how to use gfortran in R to library package so the > problem is still unsolved. > > > > > In detail, i can't understand the following steps because i am a medical > student and know a little about professional CS. > > > > > "This binary installs into /opt/R/arm64/gfortran with an additional symlink > in /opt/R/arm64/bin/gfortran. To unpack use > > tar fxz gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C / > > > (prefix with sudo if you need admin permissions to write to /opt/R/arm64). To > use set > > export PATH=$PATH:/opt/R/arm64/gfortran/bin > > > In addition, /opt/R/arm64/gfortran/SDK has to point to your macOS SDK. The > binary above points to MacOSX11.sdk of Xcode Command Line Tools, but you may > need to change it to match your installation. We include a script > gfortran-update-sdk in the above tar ball that you can simply run (prefix > with sudo if you require admin permissions). > > This build has been configured with: > > ../gcc-darwin-arm64/configure --prefix=/opt/R/arm64/gfortran > --enable-languages=c,fortran \ > --with-gmp=/opt/R/arm64 --with-mpc=/opt/R/arm64 --with-mpfr=/opt/R/arm64 \ > --with-sysroot=/opt/R/arm64/gfortran/SDK" > Sincerely Yours > Bowen Lai > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=gMuHajvpZe3IR5u1PjVWd7QfLsJ0e8G-XnVqwDn9OaFkN8mSzr_84YXGXJ8kbAkP&s=aL90rCYLJPHYRikdgnvybzrxmENyuXx5saOUuW93yZs&e= _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=gMuHajvpZe3IR5u1PjVWd7QfLsJ0e8G-XnVqwDn9OaFkN8mSzr_84YXGXJ8kbAkP&s=aL90rCYLJPHYRikdgnvybzrxmENyuXx5saOUuW93yZs&e= [[alternative HTML version deleted]]
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