[R-SIG-Mac] Unable to library package "affy"

[Jennifer Wokaty]

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-bounces using r-project.org> on behalf of Ken Beath <ken using kjbeath.com.au>
Sent: Tuesday, December 13, 2022 5:27 AM
To: Bowen Lai <bwlaispine using 163.com>
Cc: r-sig-mac using r-project.org <r-sig-mac using 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 <bwlaispine using 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
>
>
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