relatively new install issue

[iwelch]

ERROR: dependency ‘fstcore’ is not available for package ‘fst’

huf_decompress.c:(.text+0x3b9f): undefined reference to `HUF_decompress4X1_usingDTable_internal_fast_asm_loop'
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: ./libZSTD.a(huf_decompress.o): relocation R_X86_64_PC32 against undefined hidden symbol `HUF_decompress4X1_usingDTable_internal_fast_asm_loop' can not be used when making a shared object
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [/usr/lib64/R/share/make/shlib.mk:10: fstcore.so] Error 1
ERROR: compilation failed for package ‘fstcore’
* removing ‘/mnt/faculty/iwelch/R/x86_64-suse-linux-gnu-library/4.3/fstcore’
ERROR: dependency ‘fstcore’ is not available for package ‘fst’
* removing ‘/mnt/faculty/iwelch/R/x86_64-suse-linux-gnu-library/4.3/fst’

The downloaded source packages are in
    ‘/var/fasttmp/RtmpvhASMO/downloaded_packages’
Warning messages:
1: In install.packages("fst") :
  installation of package ‘fstcore’ had non-zero exit status
2: In install.packages("fst") :
  installation of package ‘fst’ had non-zero exit status

platform       x86_64-suse-linux-gnu       
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          3.1                         
year           2023                        
month          06                          
day            16                          
svn rev        84548                       
language       R                           
version.string R version 4.3.1 (2023-06-16)
nickname       Beagle Scouts               
> R.Version

[MarcusKlik]

Hi @iwelch, thanks for reporting your issue.

The fstcore package has just been updated on CRAN and as per CRAN request the explicit C++11 specification has been removed in the new version.

Could you check which gcc version you have on your system to compile the package?

gcc --version 

you could try adding the following line to your custom Makevars (~/.R/Makevars) and see if that solves your problem?

CXX_STD = CXX11

thanx!

[MarcusKlik]

Hi @iwelch, I believe your issue is related to failing to compile assembler code in the fstcore package on your system.

Could you try to install fstcore from the develop branch and see if it compiles correctly?

devtools::install_github("fstpackage/fstcore", ref = "develop")

I've added addition platforms to the github runner of fstcore to catch this problem in the future.

[iwelch]

hi mark --- that's not so easy. I tried to install devtools, but it says

ERROR: dependency 'pkgdown' is not available for package 'devtools'

• removing '/mnt/faculty/iwelch/R/x86_64-suse-linux-gnu-library/4.3/devtools'

this is because harfbuzz is missing, and I do not have sudo privileges on this machine.

I just retried the plain install, and it was still broken.

regards,

/ivo

Ivo Welch @.***) http://www.ivo-welch.info/ J. Fred Weston Distinguished Professor, UCLA Anderson

On Fri, Dec 1, 2023 at 4:10 AM Mark Klik @.***> wrote:

Hi @iwelch https://github.com/iwelch, I believe your issue is related to failing to compile assembler code in the fstcore package on your system.

Could you try to install fstcore from the following branch and see if it compiles correctly?

devtools::install_github("MarcusKlik/fstcore", ref = "asssembly-compile")

— Reply to this email directly, view it on GitHub https://github.com/fstpackage/fst/issues/279#issuecomment-1836015096, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKCJU2LOHCYILCCCKHZMALYHHCF3AVCNFSM6AAAAABACLORW6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZWGAYTKMBZGY . You are receiving this because you were mentioned.Message ID: @.***>

[MarcusKlik]

Hi @iwelch, a new release of fstcore is submitted to CRAN where I have disabled the (unused) assembler optimization in ZSTD that is causing the compiler error that you see. Thanks again for reporting!

[iwelch]

thanks a lot, mark. works great now. fst is a great package and I use it a lot for important work!!

(the only aspect I wish fst had is a unix command line (cli) text streamer, e.g., if I want to operate on a data set in perl or C or ... without the need for R. right now, I convert to .csv.gz, then operate in C, then convert back to fst.)

regards,

/ivo

-- Ivo Welch @.***)

On Sun, Dec 3, 2023 at 8:47 AM Mark Klik @.***> wrote:

Hi @iwelch https://github.com/iwelch, a new release of fstcore is submitted to CRAN where I have disabled the (unused) assembler optimization in ZSTD that is causing the compiler error that you see. Thanks again for reporting!

— Reply to this email directly, view it on GitHub https://github.com/fstpackage/fst/issues/279#issuecomment-1837534386, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKCJU7IG76ORIDW4PPC6LTYHSTWNAVCNFSM6AAAAABACLORW6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZXGUZTIMZYGY . You are receiving this because you were mentioned.Message ID: @.***>

[MarcusKlik]

Hi @iwelch, you mean a command line interpreter that can read fst files and stream them or convert them to another format?

(that might be an interesting addition to fst's underlying C++ library fstlib)

[iwelch]

Just stream in ascii format. In csv like format, a plus.

$ fst2txt my.fst … $ fst2txt -csv my.fst …

For quick slurp…

On Wed, Dec 6, 2023 at 8:44 AM Mark Klik @.***> wrote:

Hi @iwelch https://github.com/iwelch, you mean a command line interpreter that can read fst files and stream them or convert them to another format?

— Reply to this email directly, view it on GitHub https://github.com/fstpackage/fst/issues/279#issuecomment-1842430738, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKCJU3KM4JSXM3XJJDVESLYIAVKBAVCNFSM6AAAAABACLORW6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBSGQZTANZTHA . You are receiving this because you were mentioned.Message ID: @.***>