Doing dry-run gives:
[zhupy@cedar1 src]$ R CMD SHLIB --dry-run closure.cpp
[mii] *Please select a module to run *R*:*
* MODULE PARENT(S)*
1 r/4.4.0 StdEnv/2023
2 r/4.3.1 StdEnv/2023
3 r/4.3.1 StdEnv/2020
4 r/4.2.2 StdEnv/2020
5 r/4.2.1 StdEnv/2020
6 r/4.1.2 StdEnv/2020
7 r/4.1.0 StdEnv/2020
8 r/4.0.5 StdEnv/2020
9 r/4.0.2 StdEnv/2020
10 r/4.0.0 StdEnv/2020
11 sagemath/9.3 StdEnv/2020
Make a selection (1-11, q aborts) [1]: 1
[mii] loading StdEnv/2023 r/4.4.0 ...
make cmd is
make -f 'Makevars' -f '/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/etc/Makeconf'
-f '/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/share/make/shlib.mk'
SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)'
SHLIB='closure.so' OBJECTS='closure.o'
make would use
g++ -std=gnu++17 -I"/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/include"
-DNDEBUG -I/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/java/17.0.6/include
-I/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/include
-I/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/include/flexiblas
-O3 -fpic -O2 -ftree-vectorize -march=x86-64-v3 -fno-math-errno -c
closure.cpp -o closure.o
if test "zclosure.o" != "z"; then \
echo g++ -std=gnu++17 -shared -L"/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/lib
" -o closure.so closure.o -L"/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/lib"
-lR; \
g++ -std=gnu++17 -shared -L"/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/lib
" -o closure.so closure.o -L"/cvmfs/
soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/lib"
-lR; \
fi
On Wed, May 21, 2025 at 6:59 PM Peiyuan Zhu <garyzh...@gmail.com> wrote:
> Unfortunately this still doesn't work.
>
> > devtools::install("/home/zhupy/projects/def-kwalley/zhupy/dst-1")
>
> ── R CMD build
> ─────────────────────────────────────────────────────────────────
>
> ✔ checking for file ‘/project/6046455/zhupy/dst-1/DESCRIPTION’ (847ms)
>
> ─ preparing ‘dst’: (17.8s)
>
> ✔ checking DESCRIPTION meta-information ...
>
> ─ cleaning src
>
> ─ checking for LF line-endings in source and make files and shell scripts
> (638ms)
>
> ─ checking for empty or unneeded directories
>
> Removed empty directory ‘dst/.idea’
>
> ─ building ‘dst_1.9.0.tar.gz’
>
> Warning: invalid uid value replaced by that for user 'nobody'
>
> Warning: invalid gid value replaced by that for user 'nobody'
>
>
>
> Running \
>
> /cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/bin/R
> \
>
> CMD INSTALL /tmp/RtmpwaSy51/dst_1.9.0.tar.gz --install-tests
>
> * installing to library ‘/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4’
>
> * installing *source* package ‘dst’ ...
>
> ** using staged installation
>
> ** libs
>
> using C++ compiler: ‘g++ (Gentoo 12.3.1_p20230526 p2) 12.3.1 20230526’
>
> g++ -std=gnu++17 -I"/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/include"
> -DNDEBUG -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'
> -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/BH/include'
> -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/RcppProgress/include'
> -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/RcppArmadillo/include'
> -I/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/java/17.0.6/include
> -I/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/include
> -I/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/include/flexiblas
> -O3 -fpic -O2 -ftree-vectorize -march=x86-64-v3 -fno-math-errno -c
> RcppExports.cpp -o RcppExports.o
>
> g++ -std=gnu++17 -I"/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/r/4.4.0/lib64/R/include"
> -DNDEBUG -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'
> -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/BH/include'
> -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/RcppProgress/include'
> -I'/home/zhupy/R/x86_64-pc-linux-gnu-library/4.4/RcppArmadillo/include'
> -I/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/java/17.0.6/include
> -I/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/include
> -I/cvmfs/
> soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/include/flexiblas
> -O3 -fpic -O2 -ftree-vectorize -march=x86-64-v3 -fno-math-errno -c
> belplauHFast.cpp -o belplauHFast.o
>
>
>
> On Wed, May 21, 2025 at 6:50 PM Peiyuan Zhu <garyzh...@gmail.com> wrote:
>
>> I saw this line from the manual:
>>
>> Flags that are already set (for example in file etcR_ARCH/Makeconf) can
>> be overridden by the environment variable MAKEFLAGS (at least for
>> systems using a POSIX-compliant make), as in (Bourne shell syntax)
>>
>> MAKEFLAGS="CFLAGS=-O3" R CMD SHLIB *.c
>>
>> I can give it a try.
>>
>>
>>
>> On Wed, May 21, 2025 at 6:44 PM Peiyuan Zhu <garyzh...@gmail.com> wrote:
>>
>>> The manual seems unreadable at this point. Every sentence has at least
>>> two words which I don't understand.
>>>
>>> That said, I was able to find the compiler flags. They're still in
>>> Makeconf in the system. I don't know how I can control this in a package.
>>>
>>> dhcp-128-189-214-31:src garyzhubc$ R CMD SHLIB --dry-run closure.cpp
>>>
>>> make cmd is
>>>
>>> make -f 'Makevars' -f
>>> '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f
>>> '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk'
>>> SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)'
>>> SHLIB='closure.so' OBJECTS='closure.o'
>>>
>>>
>>> make would use
>>>
>>> if test "zclosure.o" != "z"; then \
>>>
>>> echo clang++ -arch x86_64 -std=gnu++17 -dynamiclib
>>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup
>>> -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/x86_64/lib -o
>>> closure.so closure.o -F/Library/Frameworks/R.framework/.. -framework
>>> R -Wl,-framework -Wl,CoreFoundation; \
>>>
>>> clang++ -arch x86_64 -std=gnu++17 -dynamiclib
>>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup
>>> -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/x86_64/lib -o
>>> closure.so closure.o -F/Library/Frameworks/R.framework/.. -framework
>>> R -Wl,-framework -Wl,CoreFoundation; \
>>>
>>> fi
>>>
>>>
>>>
>>> On Wed, May 21, 2025 at 2:22 PM Kevin Ushey <kevinus...@gmail.com>
>>> wrote:
>>>
>>>> Peiyuan,
>>>>
>>>> Respectfully -- RTFM.
>>>>
>>>> https://cran.r-project.org/doc/manuals/R-exts.html#Using-Makevars
>>>>
>>>> https://cran.r-project.org/doc/manuals/R-admin.html#Customizing-package-compilation
>>>>
>>>> The compilation flags are coming either from your R installation's
>>>> etc/Makeconf, etc/Makevars.site, a user Makevars, or the package's
>>>> Makevars.
>>>>
>>>> You can also use R CMD SHLIB --dry-run to figure out what `make`
>>>> invocation R is using, so you can know where these compiler flags are
>>>> coming from. For example:
>>>>
>>>> $ R CMD SHLIB --dry-run example.cpp
>>>> make cmd is
>>>> make -f 'Makevars' -f
>>>> '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f
>>>> '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' -f
>>>> '/Users/kevin/.R/Makevars' SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)'
>>>> SHLIB_LD='$(SHLIB_CXXLD)' SHLIB='example.so' OBJECTS='example.o'
>>>>
>>>> Kevin
>>>>
>>>> On Wed, May 21, 2025 at 2:12 PM Dirk Eddelbuettel <e...@debian.org>
>>>> wrote:
>>>> >
>>>> >
>>>> > On 21 May 2025 at 13:55, Peiyuan Zhu wrote:
>>>> > | Thanks Kasper, but I don’t know how exactly to accomplish this. As
>>>> Dirk says
>>>> > | the system overwrites it every time.
>>>> >
>>>> > That is *not* what Dirk said.
>>>> >
>>>> > Dirk
>>>> >
>>>> > --
>>>> > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>>>> >
>>>> > ______________________________________________
>>>> > R-package-devel@r-project.org mailing list
>>>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>
>>>
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