Re: [R-SIG-Mac] Please test R 4.3.0 RC, more information below
About the Fortran compiler: Den 2023-04-18 kl. 05:18, skrev Simon Urbanek: Dear Mac users, Package developers, please check the CRAN result pages for your package to make sure it passes checks. Also please note that we are now using a universal GNU Fortran compiler that works both on Intel and arm64 Macs - you can download an Apple Installer from https://mac.r-project.org/tools/ I have GNU Fortran (GCC) 12.0.1 20220312 (experimental) in /opt/R/arm64/gfortran/bin/gfortran Should it be uninstalled/removed in some way before installing gfortran-12.2-universal.pkg, and if so, how? Thanks, Göran Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Warnings installing from source
When running R CMD INSTALL xxx.tar.gz I get a lot of warnings, the first being ld: warning: -undefined dynamic_lookup may not work with chained fixups followed by several of the type ld: warning: could not create compact unwind for _yyy_: registers 72 and 73 not saved contiguously in frame where 'yyy' stands for names of fortran functions/subroutines in the package xxx. I have installed the usual tools, including gfortran, from https://mac.r-project.org/tools/ The C compiler is clang (14.0.0), for reasons I have forgotten. However, the package loads an runs as usual(?), so I wonder what I should do about it? Nothing? But what do the warnings mean? Thanks, Göran PS. No warnings on Ubuntu. > sessionInfo() R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.0.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib locale: [1] sv_SE.UTF-8/sv_SE.UTF-8/sv_SE.UTF-8/C/sv_SE.UTF-8/sv_SE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.2.2 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [External] Rmpfr crashes on Mac
I have the oldest MacBook Pro: mid 2010. Is it too early to upgrade to
an M1Max one, for R purposes? Anyway, I get (this is R, but RStudio
aborts too):
> x1 <- mpfr(-50, 200)
*** caught illegal operation ***
address 0x10fd8c23b, cause 'illegal opcode'
Traceback:
1: mpfr.default(-50, 200)
2: mpfr(-50, 200)
General info:
> R.version
_
platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 1.2
year 2021
month 11
day01
svn rev81115
language R
version.string R version 4.1.2 (2021-11-01)
nickname Bird Hippie
>
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.2
> system("system_profiler SPHardwareDataType SPSoftwareDataType")
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro6,2
Processor Name: Intel Core i7
Processor Speed: 2,66 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 8 GB
Boot ROM Version: 99.0.0.0.0
SMC Version (system): 1.58f17
Serial Number (system): W8042281AGZ
Hardware UUID: A1D55A7E-9CD1-59BD-AB78-E5B2518D4940
Sudden Motion Sensor:
State: Enabled
Software:
System Software Overview:
System Version: macOS 10.13.6 (17G14042)
Kernel Version: Darwin 17.7.0
Boot Volume: Samsung SSD
Boot Mode: Normal
Computer Name: MBP (2)
User Name: Göran Broström (gobr0002)
Secure Virtual Memory: Enabled
System Integrity Protection: Enabled
Time since boot: 25 minutes
Den 2021-11-29 kl. 06:43, skrev Kevin Ushey:
Okay, I've reproduced the crash on my 2013 Intel MacBook Pro. In this case,
the issue reproduces more readily because RStudio is calling str() behind
the scenes (which is the cause of the crash in this case). So, a plain R
reproducible example:
library(Rmpfr)
x <- mpfr(-50.1, 200)
str(x)
and I see:
str(x)
Class 'mpfr' [package "Rmpfr"] of length 1 and precision 200
*** caught illegal operation ***
address 0x112833ed5, cause 'illegal opcode'
Traceback:
1: .mpfr2str(x, digits, maybe.full = maybe.full, base = base)
2: formatMpfr(object, digits = digits.d, drop0trailing = drop0trailing,
...)
3: str.mpfr(x)
4: str(x)
From lldb:
* thread #1, queue = 'com.apple.main-thread', stop reason =
EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
frame #0: 0x000107ec7ed5 Rmpfr.so`mpfr_get_str_aux + 165
Rmpfr.so`mpfr_get_str_aux:
-> 0x107ec7ed5 <+165>: adcxq %rsi, %rcx
0x107ec7edb <+171>: movq %r10, %rdi
0x107ec7ede <+174>: movq %r8, %rsi
0x107ec7ee1 <+177>: movq %r10, %rbx
and relevant part of the backtrace:
(lldb) bt
* thread #1, queue = 'com.apple.main-thread', stop reason =
EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
* frame #0: 0x000107ec7ed5 Rmpfr.so`mpfr_get_str_aux + 165
frame #1: 0x000107ec78da Rmpfr.so`mpfr_get_str + 2890
frame #2: 0x000107eb9c9e Rmpfr.so`mpfr2str(x=0x0001053ed768,
digits=, maybeFull=, base=) at
convert.c:608:2 [opt]
< ... >
If I understand correctly, 'adcx' was introduced with Broadwell CPUs (so,
October 2014) and so that could explain why I'm seeing this crash. It'd be
helpful if others could try to verify with newer / older macOS machines,
though.
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Best,
Kevin
On Sun, Nov 28, 2021 at 6:22 PM Simon Urbanek
wrote:
Kevin,
that is a different story, yes, Rosetta2 is incomplete - the advice on M1
is to use native R.
Cheers,
Simon
On Nov 29, 2021, at 12:30 PM, Kevin Ushey wrote:
I can reproduce something similar on my M1 macOS machine, when using the
x86_64 build of R. I see:
x1 <- mpfr(-50, 200)
*** caught illegal operation ***
address 0x10c5f623b, cause 'illegal opcode'
This is with the binary of Rmpfr 0.8-7 as from CRAN, with R 4.1.2. Here's
what LLDB says:
* thread #1, queue = 'com.apple.main-thread', stop reason =
EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
frame #0: 0x00010f69c23b Rmpfr.so`mpfr_set_d + 43
Rmpfr.so`mpfr_set_d:
-> 0x10f69c23b <+43>: vucomisd %xmm0, %xmm0
0x10f69c23f <+47>: jp 0x10f69c39a
Re: [R-SIG-Mac] PCRE JIT compilation error
No problem at all with 10.13.6. G, Den 2020-04-01 kl. 15:20, skrev Bryan Hanson: Having played with things a bit more, this message appears all over the place as people are beginning to report. Another simple way to trigger it is to do: ?dist Bryan On Apr 1, 2020, at 8:36 AM, Matthias Krawutschke wrote: Hello together, i´ve got this message too, but my systems show me first the list of all installed libraries on my MAC. Best regards and take care…. Matthias Krawutschke, Dipl. Inf. Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team Infrastruktur Server und Storage Spezialized: High-Performance-Computing and Kubernetes Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-153065, Fax: +49 331 977-1750 Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html -Ursprüngliche Nachricht- Von: R-SIG-Mac Im Auftrag von Bryan Hanson Gesendet: Mittwoch, 1. April 2020 13:30 An: r-sig-mac R Betreff: [R-SIG-Mac] PCRE JIT compilation error On a fresh install of the binary from mac.r-project.org, if I simply do: library() I see: R > library() There were 30 warnings (use warnings() to see them) R > warnings() Warning messages: 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error 'no more memory' 2: In FUN(X[[i]], ...) : PCRE JIT compilation error 'no more memory' etc. The usual window with installed packages does open. Starting the conversation here on the Mac list, though it may be a bigger problem. Thanks, Bryan Prof. Bryan Hanson (emeritus) Dept of Chemistry & Biochemistry DePauw University Greencastle IN 46135 USA Web: academic.depauw.edu/~hanson/index.html Repo: github.com/bryanhanson Nerdy Blog: ChemoSpec.org The Twit: @ProfBryanHanson I’m usually @ -4 GMT/UTC R > sessionInfo() R version 4.0.0 alpha (2020-03-29 r78109) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base loaded via a namespace (and not attached): [1] compiler_4.0.0 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!
Hello JJB, Den 2020-04-01 kl. 15:30, skrev Balamuta, James Joseph: Simon, Thanks for the overview! A few quick questions: 1. Compiler-wise, the external clang compiler requirement was removed and, so, there is no guarantee of OpenMP on macOS again? 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new push for increased security by Apple? One reason is that I am on 10.13(.6) without possibility to upgrade to 10.14 (MacBook Pro & Air, 2010). 3. How likely is the oldest system requirement to be bumped in a patch release? Hopefully very unlikely;) Best, Göran PS. I have installed and run the 4.0.0 binary without any problem (so far). Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more than happy to help! Best, JJB On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" wrote: Dear Mac users, R 4.0.0 will be using an entirely new toolchain, entirely new build system on entirely new macOS version and hardware. Therefore I would like to ask you kindly to test the binaries from https://mac.R-project.org before the release as much as you can. Raising any issues after the release is too late! So please, please, test the pre-releases. Report any issues either directly to me or this mailing list. The nightly builds are signed, but not necessarily notarized. However, the build fulfils Apple's conditions and is known to pass notarization (in fact the the package available for download today is actually notarized) so it should be a good test for the release which will be notarized and should work on Catalina. For those that want to replicate our setup - technical details: we are now building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple command line tools (this should make it easy to replicate the setup using Travis, for example). All 3rd party libraries that CRAN uses are available in http://mac.r-project.org/libs-4/ The new R build system is in https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4 Packages build system has not changed and is in https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages We also plan to have a mac-builder available with similar function as the win-builder where pre-submission tests can be performed and potentially a Travis template. Please test R pre-releases and provide feedback! Thanks, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R-devel from source (solved)
Here is the report I promised. I followed the path below: 1. Got source from CRAN. 2. Read instructions under "Download R for (Mac) OS X" (shouldn't that read "Download R for macOS" nowadays?). Especially the note Important: "If you wish to compile R packages ..., see the tools directory." 3. In the tools directory: Download and install clang-7.0.0.pkg (I see now that I should have chosen clang-8.0.0 for R 3.7.0, which is R-devel?). Also download and install gfortran-6.1.pkg (It says: "To be used with El Capitan builds of R.", which worried me a little, since I am on High Sierra, but there were no alternatives.) With this setup I got my first reported error. Thanks to Peter, I went on to https://cran.r-project.org/doc/manuals/r-release/Radmin.html#macOS, where I read -- One way to use these builds with a binary distribution of R is to have a ~/.R/Makevars file similar to (El Capitan) FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm or (Sierra or High Sierra) FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -- I naively chose the "Sierra or High Sierra" alternative, but that was wrong as you can see: It apparently refers to gfortran 6.3, so I switched to the the "El Capitan" alternative. The final error message was then something about 'unable to compile mixed C and Fortran code', and that was fixed by changing LDFLAGS="-L/usr/local/clang7/lib -L/usr/local/lib" to LDFLAGS="-L/usr/local/clang7/lib -L/usr/local/gfortran/lib -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0" and voila, ./configure run without complaints! The later build also went smoothly (but I had to install java). So, to sum up, there seems to be some discrepancy between the two instruction sets I tried to follow. Göran Den 2019-08-19 kl. 00:06, skrev Göran Broström: Den 2019-08-18 kl. 22:16, skrev peter dalgaard: /usr/local/clang7 is likely a better place to look. Check out Appendix C.3 of the R Inst. manual: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS That's better! After correcting some obvious(?) errors(?) in that page, ./configure run without errors! (Had only read mac.r-procject.org/tools/ so far). After a night's sleep I will 'make'. I'll report back to r-sig-mac. Thanks, Göran -pd On 18 Aug 2019, at 21:35 , Göran Broström wrote: Update: There is a libgcc_s.1.dylib in /usr/lib, as a symlink to /usr/lib/libSystem.B.dylib. Is that one useful? Göran Den 2019-08-18 kl. 18:54, skrev Göran Broström: Thanks Peter, The tripping lines are here configure:24611: checking size of size_t configure:24616: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib conftest.c -ldl -lm >\ &5 configure:24616: $? = 0 configure:24616: ./conftest dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib Referenced from: /Users/gb/R/src/R-devel/./conftest Reason: image not found so it seems as if my installation of tools is lacking an essential part (/usr/local/lib/libgcc_s.1.dylib). I'll look around, but any suggestion is welcome! Göran Den 2019-08-18 kl. 17:56, skrev peter dalgaard: I can't claim to understand this, but on my system of same age, using system clang, configure does complete. It does get that error on line 23748, but that, and several similar subsequent tests just end up returning "yes". configure:23748: checking for size_t configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c:118:21: error: expected expression if (sizeof ((size_t))) ^ 1 error generated. [..snip..] configure:23748: result: yes (as usual, configure code is nigh on unreadable, but I think the logic is that the size_t type exists if you can do "sizeof (size_t)", but not "sizeof ((size_t))", so the error is expected.) The line that trips you up comes later: configure:24611: checking size of size_t configure:24616: gcc -arch x86_64 -o conftest -g -O2 -I/usr/local/include -L/usr/ local/lib conftest.c -ldl -lm >&5 configure:24616: $? = 0 configure:24616: ./conftest configure:24616: $? = 0 configure:24630: result: 8 so that is where you should look for clues (or at least tell us what it says there). -pd On 18 Aug 2019, at 13:34 , Göran Broström wrote: Hello, I'm (for the first time) trying to build R-devel from source (to be able to check my CRAN packages on a Mac), but it breaks already after gobr0002@MBP-2:~/R/src/R-devel$ ./configure with checking size of size_t... configure: error: in `/Users/gb/R/src/R-deve
Re: [R-SIG-Mac] Building R-devel from source
Den 2019-08-19 kl. 09:52, skrev Uwe Ligges: On 19.08.2019 00:06, Göran Broström wrote: Den 2019-08-18 kl. 22:16, skrev peter dalgaard: /usr/local/clang7 is likely a better place to look. Check out Appendix C.3 of the R Inst. manual: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS That's better! After correcting some obvious(?) errors(?) in that page, ./configure run without errors! (Had only read mac.r-procject.org/tools/ so far). Can you report these "obvious(?) errors(?)" so they can be fixed? As I promised, a report will come. Probably later today. Best, Göran Best, Uwe After a night's sleep I will 'make'. I'll report back to r-sig-mac. Thanks, Göran -pd On 18 Aug 2019, at 21:35 , Göran Broström wrote: Update: There is a libgcc_s.1.dylib in /usr/lib, as a symlink to /usr/lib/libSystem.B.dylib. Is that one useful? Göran Den 2019-08-18 kl. 18:54, skrev Göran Broström: Thanks Peter, The tripping lines are here configure:24611: checking size of size_t configure:24616: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib conftest.c -ldl -lm >\ &5 configure:24616: $? = 0 configure:24616: ./conftest dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib Referenced from: /Users/gb/R/src/R-devel/./conftest Reason: image not found so it seems as if my installation of tools is lacking an essential part (/usr/local/lib/libgcc_s.1.dylib). I'll look around, but any suggestion is welcome! Göran Den 2019-08-18 kl. 17:56, skrev peter dalgaard: I can't claim to understand this, but on my system of same age, using system clang, configure does complete. It does get that error on line 23748, but that, and several similar subsequent tests just end up returning "yes". configure:23748: checking for size_t configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c:118:21: error: expected expression if (sizeof ((size_t))) ^ 1 error generated. [..snip..] configure:23748: result: yes (as usual, configure code is nigh on unreadable, but I think the logic is that the size_t type exists if you can do "sizeof (size_t)", but not "sizeof ((size_t))", so the error is expected.) The line that trips you up comes later: configure:24611: checking size of size_t configure:24616: gcc -arch x86_64 -o conftest -g -O2 -I/usr/local/include -L/usr/ local/lib conftest.c -ldl -lm >&5 configure:24616: $? = 0 configure:24616: ./conftest configure:24616: $? = 0 configure:24630: result: 8 so that is where you should look for clues (or at least tell us what it says there). -pd On 18 Aug 2019, at 13:34 , Göran Broström wrote: Hello, I'm (for the first time) trying to build R-devel from source (to be able to check my CRAN packages on a Mac), but it breaks already after gobr0002@MBP-2:~/R/src/R-devel$ ./configure with checking size of size_t... configure: error: in `/Users/gb/R/src/R-devel': configure: error: cannot compute sizeof (size_t) See `config.log' for more details Some 'details' regarding size_t: configure:23748: checking for size_t configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c: In function 'main': conftest.c:116:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ My MacBook Pro is old (2010), so I am stuck with MacOS 10.13.6, XCode 10.1. I'm using clang 7.0.0 and fortran 6.1.0. Do I need to buy a new Mac? Thanks, Göran ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R-devel from source
Den 2019-08-18 kl. 22:16, skrev peter dalgaard: /usr/local/clang7 is likely a better place to look. Check out Appendix C.3 of the R Inst. manual: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS That's better! After correcting some obvious(?) errors(?) in that page, ./configure run without errors! (Had only read mac.r-procject.org/tools/ so far). After a night's sleep I will 'make'. I'll report back to r-sig-mac. Thanks, Göran -pd On 18 Aug 2019, at 21:35 , Göran Broström wrote: Update: There is a libgcc_s.1.dylib in /usr/lib, as a symlink to /usr/lib/libSystem.B.dylib. Is that one useful? Göran Den 2019-08-18 kl. 18:54, skrev Göran Broström: Thanks Peter, The tripping lines are here configure:24611: checking size of size_t configure:24616: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib conftest.c -ldl -lm >\ &5 configure:24616: $? = 0 configure:24616: ./conftest dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib Referenced from: /Users/gb/R/src/R-devel/./conftest Reason: image not found so it seems as if my installation of tools is lacking an essential part (/usr/local/lib/libgcc_s.1.dylib). I'll look around, but any suggestion is welcome! Göran Den 2019-08-18 kl. 17:56, skrev peter dalgaard: I can't claim to understand this, but on my system of same age, using system clang, configure does complete. It does get that error on line 23748, but that, and several similar subsequent tests just end up returning "yes". configure:23748: checking for size_t configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c:118:21: error: expected expression if (sizeof ((size_t))) ^ 1 error generated. [..snip..] configure:23748: result: yes (as usual, configure code is nigh on unreadable, but I think the logic is that the size_t type exists if you can do "sizeof (size_t)", but not "sizeof ((size_t))", so the error is expected.) The line that trips you up comes later: configure:24611: checking size of size_t configure:24616: gcc -arch x86_64 -o conftest -g -O2 -I/usr/local/include -L/usr/ local/lib conftest.c -ldl -lm >&5 configure:24616: $? = 0 configure:24616: ./conftest configure:24616: $? = 0 configure:24630: result: 8 so that is where you should look for clues (or at least tell us what it says there). -pd On 18 Aug 2019, at 13:34 , Göran Broström wrote: Hello, I'm (for the first time) trying to build R-devel from source (to be able to check my CRAN packages on a Mac), but it breaks already after gobr0002@MBP-2:~/R/src/R-devel$ ./configure with checking size of size_t... configure: error: in `/Users/gb/R/src/R-devel': configure: error: cannot compute sizeof (size_t) See `config.log' for more details Some 'details' regarding size_t: configure:23748: checking for size_t configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c: In function 'main': conftest.c:116:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ My MacBook Pro is old (2010), so I am stuck with MacOS 10.13.6, XCode 10.1. I'm using clang 7.0.0 and fortran 6.1.0. Do I need to buy a new Mac? Thanks, Göran ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R-devel from source
Thanks Peter, The tripping lines are here configure:24611: checking size of size_t configure:24616: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib conftest.c -ldl -lm >\ &5 configure:24616: $? = 0 configure:24616: ./conftest dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib Referenced from: /Users/gb/R/src/R-devel/./conftest Reason: image not found so it seems as if my installation of tools is lacking an essential part (/usr/local/lib/libgcc_s.1.dylib). I'll look around, but any suggestion is welcome! Göran Den 2019-08-18 kl. 17:56, skrev peter dalgaard: I can't claim to understand this, but on my system of same age, using system clang, configure does complete. It does get that error on line 23748, but that, and several similar subsequent tests just end up returning "yes". configure:23748: checking for size_t configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -arch x86_64 -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c:118:21: error: expected expression if (sizeof ((size_t))) ^ 1 error generated. [..snip..] configure:23748: result: yes (as usual, configure code is nigh on unreadable, but I think the logic is that the size_t type exists if you can do "sizeof (size_t)", but not "sizeof ((size_t))", so the error is expected.) The line that trips you up comes later: configure:24611: checking size of size_t configure:24616: gcc -arch x86_64 -o conftest -g -O2 -I/usr/local/include -L/usr/ local/lib conftest.c -ldl -lm >&5 configure:24616: $? = 0 configure:24616: ./conftest configure:24616: $? = 0 configure:24630: result: 8 so that is where you should look for clues (or at least tell us what it says there). -pd On 18 Aug 2019, at 13:34 , Göran Broström wrote: Hello, I'm (for the first time) trying to build R-devel from source (to be able to check my CRAN packages on a Mac), but it breaks already after gobr0002@MBP-2:~/R/src/R-devel$ ./configure with checking size of size_t... configure: error: in `/Users/gb/R/src/R-devel': configure: error: cannot compute sizeof (size_t) See `config.log' for more details Some 'details' regarding size_t: configure:23748: checking for size_t configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 configure:23748: $? = 0 configure:23748: gcc -c -g -O2 -I/usr/local/include conftest.c >&5 conftest.c: In function 'main': conftest.c:116:21: error: expected expression before ')' token if (sizeof ((size_t))) ^ My MacBook Pro is old (2010), so I am stuck with MacOS 10.13.6, XCode 10.1. I'm using clang 7.0.0 and fortran 6.1.0. Do I need to buy a new Mac? Thanks, Göran ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing package from source
2011/5/8 Simon Urbanek simon.urba...@r-project.org There is a lot of missing pieces, but I bet that your package links unversioned libatlas-MacPro.dylib instead of libRblas.dylib and you don't have the appropriate symlinks in x86_64. Yes and No(?). In x86_64, there is a symlink libRblas.dylib - ../libRblas.dylib, and in ..: libRblas.dylib - libatlas-MacPro.dylib And similarly in i386 and ppc. Shouldn't that work like your suggestion b)? It doesn't. (Just for the record: this is your mileage may vary setup and is NOT what you get when you install R). There are several solutions: a) switch back to R BLAS when building your package (this is the default in normal R) This works. b) make a symlink from to all sub-arch directories (i386, x86_64 possibly ppc) to libatlas-MacPro.dylib. This is a just a hack - your binaries won't work on anyone else's machines. This doesn't work either; maybe I misunderstood? I did, in x86_64, ppc, and i386: ln -sfn ../libatlas-MacPro.dylib libRblas.dylib I would prefer this to a) since it avoids switching back and forth; I don't care about moving binaries. Thanks for your help, Göran c) add versioned path to your libatlas-MacPro.dylib using install_name_tool -id, preferably pointing to libRblas and NOT the MacPro variant, i.e. for R 2.13.x: install_name_tool -id /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libRblas.dylib libatlas-MacPro.dylib Cheers, Simon On May 7, 2011, at 6:07 PM, Göran Broström wrote: I'm new to the Mac, but have used R under Linux for about 15 years. Now R CMD INSTALL skel_1.0-2.tar.gz fails with error message Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel/libs/x86_64/skel.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel/libs/x86_64/skel.so, 6): Library not loaded: libatlas-MacPro.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel/libs/x86_64/skel.so Reason: image not found Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel' * restoring previous '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel' -- The 'libatlas-MacPro.dylib' seems to be the culprit, but who knows? I installed it just before this, following Simon's recipe from a post to this list in October 2010. skel is a private package which installs under Linux and Windose without problems. sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/C/C/C/en_US.UTF-8/C attached base packages: [1] stats graphics grDevices utils datasets methods base I have also installed gfortran, Xcode, etc. Göran [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Installing package from source
I'm new to the Mac, but have used R under Linux for about 15 years. Now R CMD INSTALL skel_1.0-2.tar.gz fails with error message Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel/libs/x86_64/skel.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel/libs/x86_64/skel.so, 6): Library not loaded: libatlas-MacPro.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel/libs/x86_64/skel.so Reason: image not found Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel' * restoring previous '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/skel' -- The 'libatlas-MacPro.dylib' seems to be the culprit, but who knows? I installed it just before this, following Simon's recipe from a post to this list in October 2010. skel is a private package which installs under Linux and Windose without problems. sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/C/C/C/en_US.UTF-8/C attached base packages: [1] stats graphics grDevices utils datasets methods base I have also installed gfortran, Xcode, etc. Göran [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
