microsoft/deployr-rserve

DeployR fork of the popular R package, Rserve.

deployr-rserve

deployr-rserve is a fork of the popular R package, Rserve, from Simon Urbanek.

This fork is based on Rserve 0.6-3.1 and adds the following features:

1. Concurrent R sessions under Rserve on the Windows platform
2. Ability to switch the execution context of the Rserve process to a specified uid/gid
3. Out-of-band control socket that supports a cancel operation on any Rserve eval operation

Installations of DeployR require deployr-rserve. The standard Rserve package does not include the necessary functionality to work with DeployR.

deployr-rserve's Issues

memory.limit on x64 windows always allocates 2GB

Compilation error on CentOS 7 with MRO-3.2.3

I'm trying to setup deployR on CentOS 7, with Microsoft R Open 3.2.3 and deployrRserve_7.4.2.
I'm actually running into a compilation error when trying to install deployRserve using R CMD INSTALL deployrRserve_7.4.2.tar.gz. Following this link I added libicu-devel to the install but it didn't resolve the issue.

Output of R CMD INSTALL deployrRserve_7.4.2.tar.gz is:

* installing to library '/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/library'
* installing *source* package 'deployrRserve' ...
checking whether to compile the server... yes
checking whether to compile the client... no
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking netinet/tcp.h usability... yes
checking netinet/tcp.h presence... yes
checking for netinet/tcp.h... yes
checking for an ANSI C-conforming const... yes
checking whether byte ordering is bigendian... no
checking whether time.h and sys/time.h may both be included... yes
checking for pid_t... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking for library containing crypt... -lcrypt
checking crypt.h usability... yes
checking crypt.h presence... yes
checking for crypt.h... yes
checking for socklen_t... yes
checking for connect... yes
checking for dlopen in -ldl... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating src/client/cxx/Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
** arch - 
gcc -std=gnu99 -I/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/include -DNDEBUG  -I/usr/local/include   -DDAEMON -Iinclude -I. -I/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/include -fpic  -g -O2  -c Rserv.c -o Rserv.o
Rserv.c: In function 'cancelValidateConn':
Rserv.c:1946:19: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
         int sfd = (int) ifd;
                   ^
Rserv.c: In function 'startThread':
Rserv.c:3007:78: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
         int iret1 = pthread_create( &cancelThread, NULL, cancelValidateConn, (void*)connfd);
                                                                              ^
gcc -std=gnu99 -I/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/include -DNDEBUG  -I/usr/local/include   -DDAEMON -Iinclude -I. -I/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/include -fpic  -g -O2  -c session.c -o session.o
gcc -std=gnu99 -I/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/include -DNDEBUG  -I/usr/local/include   -DDAEMON -Iinclude -I. -I/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/include -fpic  -g -O2  -c md5.c -o md5.o
gcc -std=gnu99 Rserv.o session.o md5.o -o Rserve -Wl,--export-dynamic -fopenmp  -L/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/lib -lR -lz -lrt -ldl -lm -licuuc -licui18n -ldl -lcrypt   -lpthread
/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
make: *** [Rserve] Error 1
ERROR: compilation failed for package 'deployrRserve'
* removing '/usr/lib64/MRO-3.2.3/R-3.2.3/lib64/R/library/deployrRserve'

Below is the docker file I'm using to build the image (starts from centOS 7 and just installs jdk, MRO and deploy-rserve):

FROM centos:7

ENV JDK_VERSION=8u73
ENV JDK_CHECKSUM=4fa29c2b099444cecd1debdd4810ea8d
ENV JAVA_HOME=/usr/java/jdk1.8.0_73
ENV MRO_CHECKSUM=c25695d574f035b37817f01a995ecd272f948a98
ENV DEPLOYR_CHECKSUM=74a91a191925193cf2406c217daaa3022bde778cd234a03a1d7e83eff78daee6

WORKDIR /opt/

RUN yum -y update &&\
    yum clean all &&\
    yum -y install wget which libicu-devel

RUN wget --no-check-certificate --no-cookies --header \
    "Cookie: oraclelicense=accept-securebackup-cookie" \
    "http://download.oracle.com/otn-pub/java/jdk/$JDK_VERSION-b02/jdk-$JDK_VERSION-linux-x64.rpm" &&\
    echo "$JDK_CHECKSUM  jdk-$JDK_VERSION-linux-x64.rpm" | md5sum -c &&\
    yum install -y "jdk-$JDK_VERSION-linux-x64.rpm" &&\
    yum clean all &&\
    rm -rf "jdk-$JDK_VERSION-linux-x64.rpm" &&\
    export JAVA_HOME=$JAVA_HOME

# MRO
RUN wget "https://mran.revolutionanalytics.com/install/mro/3.2.3/MRO-3.2.3.el7.x86_64.rpm" &&\
    echo "$MRO_CHECKSUM  MRO-3.2.3.el7.x86_64.rpm" | sha1sum -c &&\
    yum install -y MRO-3.2.3.el7.x86_64.rpm &&\
    rm -rf MRO-3.2.3.el7.x86_64.rpm

# deployR-rserve
RUN wget "https://github.com/deployr/deployr-rserve/releases/download/v7.4.2/deployrRserve_7.4.2.tar.gz" &&\
    R CMD INSTALL deployrRserve_7.4.2.tar.gz &&\
    rm -rf deployrRserve_7.4.2.tar.gz

just before trying to install deployr-rserve, output of rpm -qa | grep -i libicu is as follows:

[root@a4b1bcdc8972 opt]# rpm -qa | grep -i libicu
libicu-devel-50.1.2-15.el7.x86_64
libicu-50.1.2-15.el7.x86_64

and regarding gcc:

[root@a4b1bcdc8972 opt]# rpm -qa | grep -i gcc   
libgcc-4.8.5-4.el7.x86_64
gcc-4.8.5-4.el7.x86_64
gcc-gfortran-4.8.5-4.el7.x86_64

The result of function isn't used

Greetings!

We've checked your source code and found some suspicious part. Maybe this code never executes but a bug is a bug)

https://github.com/Microsoft/deployr-rserve/blob/8b75ec4296399926df230fc5db66e45e17e9dc82/Rserve/src/client/java-old/REXP.java#L1040

        if (s.indexOf('\\')>=0)
            s.replaceAll("\\","\\\\");
        if (s.indexOf('"')>=0)
            s.replaceAll("\"", "\\\"");

The value of variable s doesn't change

This bug is found by Echelon team with AppChecker static analyzer

This repo is missing important files

There are important files that Microsoft projects should all have that are not present in this repository. A pull request has been opened to add the missing file(s). When the pr is merged this issue will be closed automatically.

Microsoft teams can learn more about this effort and share feedback within the open source guidance available internally.

Merge this pull request

MD5 checksum error

Installing on a Windows 2012 Server and version 7.4.2 installs perfectly, however version 8.0.5 returns the following error:
file 'Rserve.exe' has the wrong MD5 checksum

I have downloaded the file multiple times on different computers and networks and the result is always the same error. I'm following the instructions posted here:
https://msdn.microsoft.com/en-us/microsoft-r/deployr-admin-diagnostics-troubleshooting#manual-package-install