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s-u / Rserve

Fast, flexible and powerful server providing access to R from many languages and systems
http://RForge.net/Rserve
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Error to run Rserve with R 3.5.0 - long vectors not supported yet: qap_encode.c:36 #102

Closed Bio7 closed 6 years ago

Bio7 commented 6 years ago

I just installed R 3.5.0 on two Macs (High Sierra, El Capitan) and tried to install the latest Rserve version:

It compiled succesfully and the server starts. At runtime however I get the following error when I try to connect the client to the Server. The client connection can't be established.

Error in run.Rserve() : long vectors not supported yet: qap_encode.c:36

https://github.com/s-u/Rserve/blob/master/src/qap_encode.c#L36

I think this has something to do with the long indexing in R?

Here the install command (I use Rserve in cooperative mode locally):

sudo PKG_CPPFLAGS=-DCOOPERATIVE R CMD INSTALL Rserve_1.8-5.tar.gz

Here the current session Info for completeness (but the error also occurs on a High Sierra laptop!):

sessionInfo()

R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.5.0

Bio7 commented 6 years ago

I searched a little bit and found in the R news some pointers for long vectors:

https://cran.r-project.org/src/base/NEWS

A detailed description of the changes can be found in this article:

https://www.sciencedirect.com/science/article/pii/S0098300416307415

So it might be possible that the LENGTH function in line 36:

https://github.com/s-u/Rserve/blob/master/src/qap_encode.c#L36

can be replaced by XLENGTH, etc.?

hideaki commented 6 years ago

I got the same error, and replacing LENGTH() with XLENGTH() as @Bio7 suggested does seem to eliminate the error.

s-u commented 6 years ago

It needs more than just the one occurrence. So I added large vector support to the QAP encoding and decoding. It would be interesting to find out why R creates a large vector for something that is actually small - could be a bug in R.

yannrichet commented 6 years ago

If it helps:

pgrech2 commented 6 years ago

Any updates, receiving same issue.

Keswiik commented 6 years ago

@pgrech2 you may be pulling an older release of Rserve if you're installing from CRAN (install.packages('Rserve')).

I ran into this issue earlier and needed to install via RForge: install.packages('Rserve',,"http://rforge.net/",type="source")

MathieuNls commented 6 years ago

Hi,

I have the same issue and, when trying to install it from rforge, I got the following error:

make -C proxy 'CC=gcc -std=gnu99' 'CPPFLAGS=-I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread' CFLAGS='-g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread' 'LIBS=-ldl -lcrypt  ' && cp -p proxy/forward .
make[1]: Entering directory '/tmp/RtmpCM1E4i/R.INSTALL1e48ccaa14/Rserve/src/proxy'
ln -sfn ../ulog.h ulog.h
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o forward.o forward.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o http.o http.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o http_tools.o http_tools.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o server.o server.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o tls.o tls.c
ln -sfn ../md5.h md5.h
ln -sfn ../sha1.h sha1.h
ln -sfn ../base64.c base64.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o websockets.o websockets.c
ln -sfn ../md5.c md5.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o md5.o md5.c
ln -sfn ../sha1.c sha1.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o sha1.o sha1.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o base64.o base64.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o date.o date.c
ln -sfn ../ulog.c ulog.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o ulog.o ulog.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o chandler.o chandler.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread -I.. -DFORKED  -DRSERVE_PKG -I. -Iinclude   -pthread  -c -o rscript.o rscript.c
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-udh3fS/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g   -pthread  -o forward forward.o http.o http_tools.o server.o tls.o websockets.o md5.o sha1.o base64.o date.o ulog.o chandler.o rscript.o -ldl -lcrypt   -lssl
/usr/bin/ld: cannot find -lssl
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:8: forward] Error 1
make[1]: Leaving directory '/tmp/RtmpCM1E4i/R.INSTALL1e48ccaa14/Rserve/src/proxy'
make: *** [Makevars:6: all] Error 2
ERROR: compilation failed for package ‘Rserve’
* removing ‘/usr/local/lib/R/site-library/Rserve’

The downloaded source packages are in
        ‘/tmp/Rtmpxix7zV/downloaded_packages’

I am running this inside the rocker/r-base:latest docker container.

yannrichet commented 6 years ago

In your last case, it seems that just libssl is missing. Probably not related to current thread.

AcaDemIQ commented 5 years ago

Excuse me, but I have this problem on the 1.8.6

Ошибка: длинные вектора еще не поддерживаются: qap_encode.c:36
Fatal error: unable to initialize the JIT

Which additional information should I send for debug analysis for you?

P.S. Sorry about my English :)

s-u commented 5 years ago

Please make sure you have the latest version, this should have been fixed in 484f5fe

quaeler commented 5 years ago

I have what appears to be the latest version, 3.5.2, on macOS 10.13.6 and this is still occurring:

Rserv started in daemon mode.
Error: long vectors not supported yet: qap_encode.c:36
Fatal error: unable to initialize the JIT

> version
               _                           
platform       x86_64-apple-darwin15.6.0   
arch           x86_64                      
os             darwin15.6.0                
system         x86_64, darwin15.6.0        
status                                     
major          3                           
minor          5.2                         
year           2018                        
month          12                          
day            20                          
svn rev        75870                       
language       R                           
version.string R version 3.5.2 (2018-12-20)
nickname       Eggshell Igloo              
>
yonibaciu commented 5 years ago

@pgrech2 you may be pulling an older release of Rserve if you're installing from CRAN (install.packages('Rserve')).

I ran into this issue earlier and needed to install via RForge: install.packages('Rserve',,"http://rforge.net/",type="source")

The above worked for me

afs091 commented 5 years ago

Greetings,

I tried rserve version 1.7.1 installed via sudo apt install cran-r-rserve and 1.8.6 installed within R via install.packages('Rserve',,"http://rforge.net/",type="source") but I am still getting the same error:

Error: long vectors not supported yet: qap_encode.c:36 Fatal error: unable to initialize the JIT

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 19.1

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=pt_PT.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.6.0 tools_3.6.0

s-u commented 5 years ago

Your sessionInfo() doesn't show Rserve - make sure you have the correct version, the error suggests you don't. Check you library paths fro older version. You'll need at least 1.8-6. You can also check with R CMD Rserve --version

afs091 commented 5 years ago

Thank you for your advice!

packageVersion('Rserve') [1] ‘1.8.6’

R CMD Rserve --version Rserve v1.7-3 ()

sudo netstat -lanp | grep 'Rserve' tcp 0 0 127.0.0.1:6311 0.0.0.0:* LISTEN 6135/Rserve

kill PID kill -9 6135

Then I launch Rserve from R

Rserve()

And everything goes well

However I don't find a way to remove the 1.7-3 version, even with R CMD REMOVE Rserve I can only target the 1.8.6 version never the 1.7-3

Thank you!

s-u commented 5 years ago

You likely installed the old version as sudo at some point, but not the new one. Check out this path:

file.path(R.home(),"bin","Rserve")

and remove it. You can also run in R:

Rserve::Rserve()

which will show you the full command to run for the currently installed version.

siddharthab commented 5 years ago

Any plans to get this fix in the 1.7 releases on CRAN? No worries if not, just curious.

Thank you.

yannrichet commented 5 years ago

In case you absolutely need it, I released a fork of 1.7 with just the LENGTH/XLENGTH patch. There: https://github.com/yannrichet/Rserve-1.7 , with sources and binaries. Tested for R 3.5 & 3.6.

Le mar. 27 août 2019 à 11:15, Siddhartha Bagaria notifications@github.com a écrit :

Any plans to get this fix in the 1.7 releases on CRAN? No worries if not, just curious.

Thank you.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/s-u/Rserve/issues/102?email_source=notifications&email_token=AAOBS3SU7XR6I5IV23BGXJDQGTWERA5CNFSM4E4S3N6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5HCQUY#issuecomment-525215827, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOBS3U35QLDEPZGTJVWJWLQGTWERANCNFSM4E4S3N6A .

siddharthab commented 5 years ago

Thanks! It will be nice to get these changes on CRAN so macOS users can get a prebuilt package.

It took me some time to figure out the right configuration options on my macOS to make it find libssl. Ultimately, I ended up disabling the proxy feature to not need libssl.

pavany666666 commented 5 years ago

Thanks guys... I had the same problem and Rserve 1.7.5 fixed it for me R 3.6.1.

Appreciate the help!

entmike commented 3 years ago

@pgrech2 you may be pulling an older release of Rserve if you're installing from CRAN (install.packages('Rserve')).

I ran into this issue earlier and needed to install via RForge: install.packages('Rserve',,"http://rforge.net/",type="source")

Just FYI this is what worked for me. Thank you.