Re: [R-sig-Debian] r-cran-rjava dependencies on debian jesse, library(rJava) fails when default-jre is missing
Hi, > Le 17 mai 2017 à 13:54, Dirk Eddelbuettel <e...@debian.org> a écrit : > > > On 17 May 2017 at 08:46, Vaidotas Zemlys wrote: > | Hi, > | > | > Le 17 mai 2017 à 00:42, Dirk Eddelbuettel <e...@debian.org> a écrit : > | > > | > > | > On 8 May 2017 at 15:39, Vaidotas Zemlys wrote: > | > | Hi, > | > | > | > | Dirk Eddelbuettel advised me to write here. Here is my original letter > to him: > | > | > | > | I would like to enquire about package r-cran-rjava on Debian jesse. It > seems that if default-jre package is not installed, but openjdk-7-jre is > installed, then library(rJava) in R fails. I’ve been bitten by this today and > I wonder whether this an issue of mine, or is this a possible bug. > | > | > | > | My server admin used apt-get update and apt-get upgrade today and R > started throwing an error that it cannot find libjvm.so, when trying to do > library(rJava). At first I thought that this is a problem of setting > JAVA_HOME, and setting it to JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 > before starting R seemed to solve the problem. But this setting was ignored > by shiny-server, so I spent some time figuring out how to force shiny-server > to respect it. Only after repeated failure I’ve noticed that LD_LIBRARY_PATH > in Sys.getenv() points to /usr/lib/jvm/default-java/jre/lib/amd64/server and > there was no directory /usr/lib/jvm/default-java/ in the system. Then I found > out that this library is provided by default-jre and when it was installed > everything start to work. Then I investigated further and found that this > package is only optional for r-cran-rjava. Hence the question. > | > | > | > | > | > | Here is my configuration: > | > | > | > | > lsb_release -a > | > | No LSB modules are available. > | > | Distributor ID: Debian > | > | Description:Debian GNU/Linux 8.8 (jessie) > | > | Release:8.8 > | > | Codename: jessie > | > | > | > | > | > | dpkg -l with relevant packages: > | > | > | > | Desired=Unknown/Install/Remove/Purge/Hold > | > | | > Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend > | > | |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) > | > | ||/ Name Version > Architecture Description > | > | > +++-=-=-=- > | > | ii r-cran-rjava 0.9-6-3 amd64 > GNU R low-level interface to Java > | > | ii r-base3.3.3-1~jessiecran.0 all > GNU R statistical computation and graphics system > | > | ii openjdk-7-jre:amd647u121-2.6.8-2~deb8u1 > amd64OpenJDK Java runtime, using Hotspot JIT > | > | ii openjdk-7-jre-headless:amd64 7u121-2.6.8-2~deb8u1 > amd64OpenJDK Java runtime, using Hotspot JIT (headless) > | > | > | > | Sorry for bothering if this is an issue from my side. > | > > | > You have the ‘jre', you need the 'jdk'. > | > > | > | But the r-cran-rjava Depends: do not mention that. Of course having > packages openjdk-7-jre and openjdk-7-jdk is not at all confusing, but that is > Java. > > I hear you but the 'jdk' is the build-depends, and needed when you want to > build other packages. The 'jre' is the smaller minimal set needed to only run > code. At least that was the idea, and at some point it worked. Maybe I need > to enlarge the Depends to use the jdk. > I think there is some misunderstanding. I was not able to run any R package which depended on rJava, which in binary form was provided by r-cran-rjava. The issue was that after the update the already installed R packages which were depending on rJava were not able to load. So build-depend would not have helped me, because I was not building any packages. Everything started to work after install of default-jre. Since I did not try to reproduce the bug on a clean install, there is a chance that my problem was self-inflicted, i.e. my admin did something not entirely advisable. I think we can close this issue. I’ve reported the issue, solicited the reaction and reaffirmed “java is tricky” idiom, so everything is cool from my side. Vaidotas Zemlys-Balevičius ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] r-cran-rjava dependencies on debian jesse, library(rJava) fails when default-jre is missing
Hi, > Le 17 mai 2017 à 00:42, Dirk Eddelbuettel <e...@debian.org> a écrit : > > > On 8 May 2017 at 15:39, Vaidotas Zemlys wrote: > | Hi, > | > | Dirk Eddelbuettel advised me to write here. Here is my original letter to > him: > | > | I would like to enquire about package r-cran-rjava on Debian jesse. It > seems that if default-jre package is not installed, but openjdk-7-jre is > installed, then library(rJava) in R fails. I’ve been bitten by this today and > I wonder whether this an issue of mine, or is this a possible bug. > | > | My server admin used apt-get update and apt-get upgrade today and R started > throwing an error that it cannot find libjvm.so, when trying to do > library(rJava). At first I thought that this is a problem of setting > JAVA_HOME, and setting it to JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 > before starting R seemed to solve the problem. But this setting was ignored > by shiny-server, so I spent some time figuring out how to force shiny-server > to respect it. Only after repeated failure I’ve noticed that LD_LIBRARY_PATH > in Sys.getenv() points to /usr/lib/jvm/default-java/jre/lib/amd64/server and > there was no directory /usr/lib/jvm/default-java/ in the system. Then I found > out that this library is provided by default-jre and when it was installed > everything start to work. Then I investigated further and found that this > package is only optional for r-cran-rjava. Hence the question. > | > | > | Here is my configuration: > | > | > lsb_release -a > | No LSB modules are available. > | Distributor ID: Debian > | Description:Debian GNU/Linux 8.8 (jessie) > | Release:8.8 > | Codename: jessie > | > | > | dpkg -l with relevant packages: > | > | Desired=Unknown/Install/Remove/Purge/Hold > | | > Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend > | |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) > | ||/ Name Version Architecture > Description > | > +++-=-=-=- > | ii r-cran-rjava 0.9-6-3 amd64 > GNU R low-level interface to Java > | ii r-base3.3.3-1~jessiecran.0 all > GNU R statistical computation and graphics system > | ii openjdk-7-jre:amd647u121-2.6.8-2~deb8u1 > amd64OpenJDK Java runtime, using Hotspot JIT > | ii openjdk-7-jre-headless:amd64 7u121-2.6.8-2~deb8u1 > amd64OpenJDK Java runtime, using Hotspot JIT (headless) > | > | Sorry for bothering if this is an issue from my side. > > You have the ‘jre', you need the 'jdk'. > But the r-cran-rjava Depends: do not mention that. Of course having packages openjdk-7-jre and openjdk-7-jdk is not at all confusing, but that is Java. Vaidotas Zemlys-Balevičius ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
[R-sig-Debian] r-cran-rjava dependencies on debian jesse, library(rJava) fails when default-jre is missing
Hi, Dirk Eddelbuettel advised me to write here. Here is my original letter to him: I would like to enquire about package r-cran-rjava on Debian jesse. It seems that if default-jre package is not installed, but openjdk-7-jre is installed, then library(rJava) in R fails. I’ve been bitten by this today and I wonder whether this an issue of mine, or is this a possible bug. My server admin used apt-get update and apt-get upgrade today and R started throwing an error that it cannot find libjvm.so, when trying to do library(rJava). At first I thought that this is a problem of setting JAVA_HOME, and setting it to JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 before starting R seemed to solve the problem. But this setting was ignored by shiny-server, so I spent some time figuring out how to force shiny-server to respect it. Only after repeated failure I’ve noticed that LD_LIBRARY_PATH in Sys.getenv() points to /usr/lib/jvm/default-java/jre/lib/amd64/server and there was no directory /usr/lib/jvm/default-java/ in the system. Then I found out that this library is provided by default-jre and when it was installed everything start to work. Then I investigated further and found that this package is only optional for r-cran-rjava. Hence the question. Here is my configuration: > lsb_release -a No LSB modules are available. Distributor ID: Debian Description:Debian GNU/Linux 8.8 (jessie) Release:8.8 Codename: jessie dpkg -l with relevant packages: Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) ||/ Name Version Architecture Description +++-=-=-=- ii r-cran-rjava 0.9-6-3 amd64 GNU R low-level interface to Java ii r-base3.3.3-1~jessiecran.0 all GNU R statistical computation and graphics system ii openjdk-7-jre:amd647u121-2.6.8-2~deb8u1 amd64 OpenJDK Java runtime, using Hotspot JIT ii openjdk-7-jre-headless:amd64 7u121-2.6.8-2~deb8u1 amd64 OpenJDK Java runtime, using Hotspot JIT (headless) Sorry for bothering if this is an issue from my side. Vaidotas Zemlys-Balevičius ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
