Hi soda, I've met the same problem with you.I fail to install the "genefilter" package with my M1 MacBook arm64 StudioI've tried several ways I could find to solve this problem, including root or modify the "/.config/Rstudio" file, and it still showedmake: /opt/R/arm64/bin/gfortran: Permission denied Since you had solved this problem by yourself (download gfortran in path /opt/R/arm64/bin), I did as the instructions.However, I could not download it in the correct path (it would be downloaded in "/User/id" instead of "/opt/R/arm64/bin") and could not open it with sudo tar fvxz even in the su rootI really hope you can help me with this.
Hello Zhusheng Zhang,Except this problem, R arm64 has many other bugs.So I unload R arm64 ,then download 'Intel 64-bit build' version. Now, I have never encountered any problems about installing package.The following answer is the same as mineyou can read it.
Download Gfortran Mac
i have solved this problem by myself.share with you.you need to download gfortran in path /opt/R/arm64/binthis website helped me: -project.org/libs-arm64/'''curl -O -project.org/libs-arm64/ -project.org/libs-arm64/gfortran-f51f1da0-darwin20.0-arm64.tar.gzsudo tar fvxz -project.org/libs-arm64/gfortran-f51f1da0-darwin20.0-arm64.tar.gz -C /'''
Hi Michael,Yes, this is what I thought. I have followed the instructions in the link provided and have downloaded Anaconda. Does Anaconda need to be in a specific place? I am still getting the same error message when I load DESeq2 into R.
If you have followed the instructions on Cheminformatics on a Mac you already have Xcode, Command Line tools and gfortran installed using Homebrew. Alternatively you can install GCC 8.3 (auto-vectorizing gcc with OpenMP) which includes gfortran (free, open source, GNU Fortran 95 compiler), gcc (GNU C) and g++ (GNU C++) compilers that can perform auto-vectorization (i.e. modify code to take advantage of AltiVec/SSE, automatically) and other sophisticated optimizations like OpenMP. There are detailed instructions here, last updated April 2019 (Mojave).
The problem persists. I googled this and found several suggestions but some seem outdated and I am not sure how to proceed. Any suggestions on how to fix this problem and get gfortran running on my M1pro?
In retrospect it might have been better to install Homebrew first. I just installed it a moment ago. In the process it downloaded Command Line Tools and put it in /Library/Developer/ . It appears that gfortran expects it there, because now gfortran works without specifying -L .
(1) In one case I needed to add -fallow-argument-mismatch to get a code to compile with the latest gfortran. This was related to compiling a large code with a subroutine that someone else wrote, that I never use, so I was not worried about coding errors.
The Xcode stuff you mentioned is for Intel OneAPI, however Intel OneAPI does not optimize for M1, so the speed of Intel Fortran will be the same as gfortran with -O0 or at best -Og. Also the Python distribution in Intel OneAPI will fail when install on M1 Mac. You need to de-select the Python part if you want to install OneAPI on M1 Mac.
However I am not sure if gfortran (or gcc) is fully compatible with M1 chip now. I personally have some code run with the same 11.2.0 gfortran on Linux well and can also run on Windows, but on M1 it can give me segment 11 error. If you have things like below (procedure point to some function) you may encounter compatibility issues.
Thanks CRquantum. I just didbrew install gfortran mpichand it installed without any problems. I recompiled and reran a serial code, and it executed about 25% faster than the version of gfortran that I installed previously without using brew. I will try compiling and running an MPI job later today or tomorrow.
Hi. I agree that this NCL page is confusing.Simple solutionGo here: Download the gfortran binary for mac (it is best to follow very easyinstructions before the link.)Then install NCL.You are good to go.Cheers,Erik Noble_______________________________________________________Erik NobleNASA Goddard Institute for Space Studies2880 Broadway, New York, NY-10025, USATel: +1 (212) 678-5512Fax: +1 (212) 678-5552E-mail: erik.noble@nasa.govWEB: GISS: _______________________________________________________On Thu, Apr 19, 2012 at 10:45 PM, Yoichi Takayama edu.auwrote:> Please improve this page:>> >> The instructions are confusing and probably not clear or contradicting.>> My system set up is:> Mac OS X 1.7> Xcode 4.3.2> ncl_ncarg-6.0.0.MacOS_10.6_64bit_gcc421.tar.gz (It is mentioned that this> should work with OSx 10.7)> gfortran 4.6.2>> Environment (.bash_profile)> export NCARG_ROOT=/usr/local> export PATH=$NCARG_ROOT/bin:$PATH> export DISPLAY=:0.0>> Created .hluresfile in $HOME>>> (1) Which gfortran?>> The page tells me to do first:>> sudo port install gcc45 +gfortran>> Then, later it tells me to do this:>> fink install gfortran>> Also, within the same section, it tells me that you got it from:>> >> All installs different versions of gfortran and probably it is not> necessary to do all these 3.>> Also, later in the part close to the end, it says that the fortran version> that the NCL binary is built against it should be installed.>> I have installed ncl_ncarg-6.0.0.MacOS_10.6_64bit_gcc421.tar.gz, but it is> not clear what version of gfortran is used (Is it the same as GCC version,> which is 4.2.1?).>> Also, when I installed Xcode 4.3.2, gcc and gfortran were installed> already.>> Also, fink install gfortran did not work, but this may be the one to use:>> fink install gfortran-shlibs [virtual library]>> This installs gcc47-shlibs-4.7.0-100. Not sure what gfortran version it> is, but I presume that gfortran is just a part of GCC and probably has the> same version number???>> By any rate, you also mentions that you have used gfortran from> >> This provides only gfortran-4.6.2-x86_64-Lion.dmg for download.>> This is the gfortran package installed last on this system.>> $ gfortran --version> GNU Fortran (GCC) 4.6.2 20111019 (prerelease)> Copyright (C) 2011 Free Software Foundation, Inc.>>>> (2) Xcode 4.3.2>> After installing Xcode 4.3.2, I have "downloaded" command line tools> previously (before installing the gfortran).>> Then ran sudo port install gcc45 +gfortran.>> However, this causes warnings to run:>> sudo xcode-select -switch /Applications/Xcode.app>> Please add this information to the note, since this had better be done> before issuing the port install command.>>> (3) limit command>> I have put limit stacksize unlimited into .bash_profile but:>> -bash: limit: command not found>> It does not seem to be installed or not in the PATH. Where could it be?>>> (4) How to install the donwloaded NCL binary>> There should be a link (or a correct order to do installation) or> consolidated note about how to install NCL from the downloaded binary.>> Typical users will go to this page but will see the link to Mac OS X> installation note "Running NCL under MacOSX" and would not find a cohesive> installation instruction there or will not think to combine the> instructions with this link:>> >> By the way, this page says it would require csh or tcsh, but Mac requires> only bash.>> Please correct it to include Mac OS X, or include the similar instruction> (step-by-step of how to install and test/run) in the "Running NCL under> MacOSX".>>> (5) Testing>> After installing all these and setting below: (by the way default shell is> bash, please correct this in your pages, too)>> export DYLD_LIBRARY_PATH=/usr/local/lib>> I had to hunt for information on how to install the NCL binary and set up> its environment as (4).>> For how to test and use, there should be a link to: (or the same should be> included on the Mac OS Note page)>> _started.shtm>> From install.shml page, these two commands worked:>> ng4ex gsun01n>> ncl gsun01n.ncl>>> However, this did not:>> $ ncargex cpex08 -clean>>> NCAR Graphics Fortran Example >> Copying cpex08.f>> Copying cpexcc.f>> Compiling and linking...> gfortran -fPIC -fno-range-check -m64 -O -o cpex08 cpexcc.f cpex08.f> -L/usr/local/lib -L/usr/X11R6/lib -lncarg -lncarg_gks -lncarg_c -lXpm -lX11> -lXext> Undefined symbols for architecture x86_64:> "__gfortran_transfer_character_write", referenced from:> _capsap_ in ccUEA5Vc.o> "__gfortran_transfer_integer_write", referenced from:> _capsap_ in ccUEA5Vc.o> "__gfortran_set_options", referenced from:> _main in ccryWR2Q.o> "__gfortran_os_error", referenced from:> _mdlnam_ in libncarg.a(mdlnam.o)> _mdlndr_ in libncarg.a(mdlndr.o)> _dpgetc_ in libncarg.a(dpgetc.o)> _dpgetr_ in libncarg.a(dpgetr.o)> _dpsetc_ in libncarg.a(dpsetc.o)> _dpsetr_ in libncarg.a(dpsetr.o)> _icfell_ in libncarg.a(icfell.o)> ...> ld: symbol(s) not found for architecture x86_64> collect2: ld returned 1 exit status>> The compile and link failed.>> Is this to do with the gfortran version used, or something else is missing> (such as header files)?>>> Thanks,> Yoichi>> --------------------------------------------------> Yoichi Takayama, PhD> Research Officer> Climate Change Research Centre> Level 4 Mathews Building> University of New South Wales> Sydney, Australia, 2052> Phone (CCRC): +61 2 9385 8963> Fax (CCRC): +61 2 9385 8969> --------------------------------------------------> UNSW ABN 57 195 873 179, CRICOS Provider 00098G> IMPORTANT: This email and any attachment(s) transmitted with it> are intended solely for the use of the addressee(s) and may contain> information that is confidential or subject to legal privilege. If you> receive this email in error, please disregard the contents of the email and> attachment(s), delete them and notify the sender immediately. Please note> that any copying, distribution or use of this email is prohibited. Any> views expressed in this message are those of the individual sender, except> where the sender expressly, and with authority, states them to be the view> of The University of New South Wales. Before opening any attachments,> please check for viruses.>>>> --------------------------------------------------> Yoichi Takayama, PhD> Research Officer> Climate Change Research Centre> Level 4 Mathews Building> University of New South Wales> Sydney, Australia, 2052> Phone (CCRC): +61 2 9385 8963> Fax (CCRC): +61 2 9385 8969> --------------------------------------------------> UNSW ABN 57 195 873 179, CRICOS Provider 00098G> IMPORTANT: This email and any attachment(s) transmitted with it> are intended solely for the use of the addressee(s) and may contain> information that is confidential or subject to legal privilege. If you> receive this email in error, please disregard the contents of the email and> attachment(s), delete them and notify the sender immediately. Please note> that any copying, distribution or use of this email is prohibited. Any> views expressed in this message are those of the individual sender, except> where the sender expressly, and with authority, states them to be the view> of The University of New South Wales. Before opening any attachments,> please check for viruses.>>> _______________________________________________> ncl-install mailing list> List instructions, subscriber options, unsubscribe:> -install>>_______________________________________________ncl-install mailing listList instructions, subscriber options, unsubscribe: -installReceived on Fri Apr 20 11:37:15 2012This message: [ Message body ]
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