[R-SIG-Mac] checking whether the C compiler works... no

Fri Sep 24 02:43:10 CEST 2021

Simon,

Thanks for your warning.  I have commented out all of my Makevars file and my R seems to be working fine.

As I mentioned, I simply followed the advice provide by data.table website.

Naresh

________________________________
From: Simon Urbanek <simon.urbanek using R-project.org>
Sent: Thursday, September 23, 2021 6:10 PM
To: Naresh Gurbuxani <naresh_gurbuxani using hotmail.com>
Cc: David Winsemius <dwinsemius using comcast.net>; r-sig-mac using r-project.org Mac <r-sig-mac using r-project.org>
Subject: Re: [R-SIG-Mac] checking whether the C compiler works... no

Before anyone actually follows this, the setup below is quite badly broken so this won't work on any normal Mac. Please do NOT set flags you don't understand even if you googled it somewhere. There is no need to modify Makevars (both versions below are bad - one is forcing locally installed clang the other gcc-11 presumably from Homebrew - neither is compatible with R releases). You should NEVER set CC/CXX in package's Makevars since the compilers have to match what R is using and R will automatically provide the correct setting, so overriding it will only break things.

Cheers,
Simon

> On Sep 24, 2021, at 8:34 AM, Naresh Gurbuxani <naresh_gurbuxani using hotmail.com> wrote:
>
> With some search on the internet, I was able to solve my problem with a small edit in Makevars file.  When installing data.table, I had added some lines to Makevars file.  These lines were pointing to clang.  The problem was fixed when it was changed to gcc.
>
> # My Makevars file new
> # Successful installation of reshape2 package
> VER=-11
> CC=gcc$(VER)
> CXX=g++$(VER)
>
> # My Makevars file old
> # These lines were recommended by data.table installation
> # Could not install reshape2 package
> CC=$(LLVM_LOC)/bin/clang -fopenmp
> CXX=$(LLVM_LOC)/bin/clang++ -fopenmp
>
> Hope this will help some user,
> Naresh
>
> From: David Winsemius <dwinsemius using comcast.net>
> Sent: Tuesday, September 7, 2021 12:02 AM
> To: Naresh Gurbuxani <naresh_gurbuxani using hotmail.com>
> Cc: r-sig-mac using r-project.org Mac <r-sig-mac using r-project.org>
> Subject: Re: [R-SIG-Mac] checking whether the C compiler works... no
>
> The   C compiler aka clang is not the same as the C++ compiler.
>
> Why don’t you install the pre-compiled version.
>
> —
> David
>
> Sent from my iPhone
>
>> On Sep 6, 2021, at 12:44 AM, Naresh Gurbuxani <naresh_gurbuxani using hotmail.com> wrote:
>> When trying to install library reshape2, I get below messages.  But I do have some other packages which depend upon C compiler (e.g., Rcpp).  How can this problem be fixed?
>>
>> Thanks,
>> Naresh
>>
>> Messages when trying to install reshape2:
>>> install.packages("reshape2", repos = "https://cran.r-project.org")
>> Installing package into ‘/usr/local/lib/R/4.1/site-library’
>> (as ‘lib’ is unspecified)
>> also installing the dependencies ‘stringi’, ‘stringr’
>>
>> trying URL 'https://cran.r-project.org/src/contrib/stringi_1.7.4.tar.gz'
>> Content type 'application/x-gzip' length 7599762 bytes (7.2 MB)
>> ==================================================
>> downloaded 7.2 MB
>>
>> trying URL 'https://cran.r-project.org/src/contrib/stringr_1.4.0.tar.gz'
>> Content type 'application/x-gzip' length 135777 bytes (132 KB)
>> ==================================================
>> downloaded 132 KB
>>
>> trying URL 'https://cran.r-project.org/src/contrib/reshape2_1.4.4.tar.gz'
>> Content type 'application/x-gzip' length 37307 bytes (36 KB)
>> ==================================================
>> downloaded 36 KB
>>
>> * installing *source* package ‘stringi’ ...
>> ** package ‘stringi’ successfully unpacked and MD5 sums checked
>> ** using staged installation
>> checking for R_HOME... /usr/local/Cellar/r/4.1.1/lib/R
>> checking for R... /usr/local/Cellar/r/4.1.1/lib/R/bin/R
>> checking for endianness... little
>> checking for R >= 3.1.0 for C++11 use... yes
>> checking for R < 3.4.0 for CXX1X flag use... no
>> checking for cat... /bin/cat
>> checking for local ICUDT_DIR... icu69/data
>> checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
>> checking whether the C compiler works... no
>> configure: error: in `/private/var/folders/97/5377j5_d207fshvjz_pz7szw0000gn/T/RtmpCOKBRx/R.INSTALL64822d9c75a/stringi':
>> configure: error: C compiler cannot create executables
>> See `config.log' for more details
>> ERROR: configuration failed for package ‘stringi’
>> * removing ‘/usr/local/lib/R/4.1/site-library/stringi’
>> ERROR: dependency ‘stringi’ is not available for package ‘stringr’
>> * removing ‘/usr/local/lib/R/4.1/site-library/stringr’
>> ERROR: dependency ‘stringr’ is not available for package ‘reshape2’
>> * removing ‘/usr/local/lib/R/4.1/site-library/reshape2’
>>
>> The downloaded source packages are in
>>     ‘/private/var/folders/97/5377j5_d207fshvjz_pz7szw0000gn/T/RtmpDOExfD/downloaded_packages’
>> Warning messages:
>> 1: In install.packages("reshape2", repos = "https://cran.r-project.org") :
>>   installation of package ‘stringi’ had non-zero exit status
>> 2: In install.packages("reshape2", repos = "https://cran.r-project.org") :
>>   installation of package ‘stringr’ had non-zero exit status
>> 3: In install.packages("reshape2", repos = "https://cran.r-project.org") :
>>   installation of package ‘reshape2’ had non-zero exit status
>>
>> My session info:
>>> sessionInfo()
>> R version 4.1.1 (2021-08-10)
>> Platform: x86_64-apple-darwin20.5.0 (64-bit)
>> Running under: macOS Big Sur 11.5.2
>>
>> Matrix products: default
>> BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.17/lib/libopenblasp-r0.3.17.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_4.1.1 tools_4.1.1
>>
>>
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