[R-SIG-Mac] code-signing for builds of R from the developer page?
Hi, It looks like the builds of R from http://mac.r-project.org/ are typically not code-signed, and so one normally gets a Gatekeeper warning when trying to install them. E.g. I see (on macOS 10.14.6): “R-3.6-branch-el-capitan.pkg” can’t be opened because it is from an unidentified developer. Your security preferences allow installation of only apps from the App Store and identified developers. Is there any chance this might change in the future? Thanks, Kevin [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problems with rJava fir R 3.6.1
Hi Thomas, I have a similar problem and I solved installing the jdk version 11.0.1 (I guess this is the version that rJava expect that you have installed). You need to search in the JDK archive to find this version. I tried the last JDK version 11.0.4 and it didn't work. After that I wrote in the terminal: R CMD javareconf And it works for me. Manuel El jue., 19 sept. 2019 a las 6:09, Thomas Knox () escribió: > I have recently installed R 3.6.1 on my MacBook running Mac OS Mojave > 10.14.5 in order to run a custom package called MH1823 (probability of > detection). This package requires me to load the following packages from > CRAN, tcltk, tcltk2, survival and xlsx. > > > > I have installed survival, xlsx and tlctk2 (i believe tcltk is embedded). > When I look at Package Manager i see that although the above packages are > installed they are not loaded. I can load survival but when I try to load > “xlsx” i get the following error message is: > > > > Error: package or namespace load failed for ‘xlsx’: > > .onLoad failed in loadNamespace() for 'rJava', details: > > call: dyn.load(file, DLLpath = DLLpath, ...) > > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': > > > dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: > /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib > > Referenced from: > /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so > > Reason: image not found > > starting httpd help server … done > > > > > > there may be a couple of hints in here. > > > > .onLoad failed in loadNamespace() for 'rJava', details suggests the > problem starts with calling rJava. > > > > the next line in the error: > > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': > > I have checked this path and see no problems, everything seems to stack up > and I find jJava.so where it is supposed to be. However in the next line: > > > dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: > /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib > > I don’t know what the number , 6 after Java.so means but have presumed > version number and may be why Java8 is not working. I also note the path > …. /JavaVirtualMachines/jdk-11.0.1.jdk/ appears as . /JavaVirtualMachines/ > 1.6.0.jdk/ > > suggesting a different build > > > > the same occurs when I try to load the local source package MH1823 > > > > When I try to load HM1823 I get the error message: > > * installing *source* package ‘mh1823’ ... > > ** using staged installation > > ** R > > ** data > > ** inst > > ** byte-compile and prepare package for lazy loading > > Error: package or namespace load failed for ‘xlsx’: > > .onLoad failed in loadNamespace() for 'rJava', details: > > call: dyn.load(file, DLLpath = DLLpath, ...) > > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': > > > dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: > /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib > > Referenced from: > /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so > > Reason: image not found > > Error: package ‘xlsx’ could not be loaded > > Execution halted > > ERROR: lazy loading failed for package ‘mh1823’ > > * removing > ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mh1823’ > > > > > > > I find that the error message is substantially the same suggesting rJava > and/or the version of Java. I have tried removing Java 8 from my machine > and installing Java 6 but don’t see any difference. It is easy to see that > Java 8 has been removed but not easy to see that 6 is installed properly as > the path names are still the same. > > > > When I try to load either tcltk or tcltk2, my instance of R stops > responding entirely. > > > > I have also installed Xquartz as I believe this is needed for Mac OS X > > > > Can anyone provide some advice on what the issue might be? I have tried > reading through the FAQ’s but not found anything to point me in the right > direction to correct the problem. > > > > Regards, > > > > Tom Knox > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr mspinol...@gmail.com Teléfono: (506) 8706 - 4662 Personal website:
Re: [R-SIG-Mac] Problems with rJava fir R 3.6.1
I try to suppress any memories of this stuff every time I have had to deal with it, but... Would "R CMD javareconf" help, maybe? -pd > On 19 Sep 2019, at 14:09 , Thomas Knox wrote: > > I have recently installed R 3.6.1 on my MacBook running Mac OS Mojave 10.14.5 > in order to run a custom package called MH1823 (probability of detection). > This package requires me to load the following packages from CRAN, tcltk, > tcltk2, survival and xlsx. > > > > I have installed survival, xlsx and tlctk2 (i believe tcltk is embedded). > When I look at Package Manager i see that although the above packages are > installed they are not loaded. I can load survival but when I try to load > “xlsx” i get the following error message is: > > > > Error: package or namespace load failed for ‘xlsx’: > > .onLoad failed in loadNamespace() for 'rJava', details: > > call: dyn.load(file, DLLpath = DLLpath, ...) > > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': > > > dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: > /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib > > Referenced from: > /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so > > Reason: image not found > > starting httpd help server … done > > > > > > there may be a couple of hints in here. > > > > .onLoad failed in loadNamespace() for 'rJava', details suggests the problem > starts with calling rJava. > > > > the next line in the error: > > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': > > I have checked this path and see no problems, everything seems to stack up > and I find jJava.so where it is supposed to be. However in the next line: > > dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: > /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib > > I don’t know what the number , 6 after Java.so means but have presumed > version number and may be why Java8 is not working. I also note the path …. > /JavaVirtualMachines/jdk-11.0.1.jdk/ appears as . > /JavaVirtualMachines/1.6.0.jdk/ > > suggesting a different build > > > > the same occurs when I try to load the local source package MH1823 > > > > When I try to load HM1823 I get the error message: > > * installing *source* package ‘mh1823’ ... > > ** using staged installation > > ** R > > ** data > > ** inst > > ** byte-compile and prepare package for lazy loading > > Error: package or namespace load failed for ‘xlsx’: > > .onLoad failed in loadNamespace() for 'rJava', details: > > call: dyn.load(file, DLLpath = DLLpath, ...) > > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': > > > dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: > /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib > > Referenced from: > /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so > > Reason: image not found > > Error: package ‘xlsx’ could not be loaded > > Execution halted > > ERROR: lazy loading failed for package ‘mh1823’ > > * removing > ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mh1823’ > >> > > > > I find that the error message is substantially the same suggesting rJava > and/or the version of Java. I have tried removing Java 8 from my machine and > installing Java 6 but don’t see any difference. It is easy to see that Java > 8 has been removed but not easy to see that 6 is installed properly as the > path names are still the same. > > > > When I try to load either tcltk or tcltk2, my instance of R stops responding > entirely. > > > > I have also installed Xquartz as I believe this is needed for Mac OS X > > > > Can anyone provide some advice on what the issue might be? I have tried > reading through the FAQ’s but not found anything to point me in the right > direction to correct the problem. > > > > Regards, > > > > Tom Knox > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Problems with rJava fir R 3.6.1
I have recently installed R 3.6.1 on my MacBook running Mac OS Mojave 10.14.5 in order to run a custom package called MH1823 (probability of detection). This package requires me to load the following packages from CRAN, tcltk, tcltk2, survival and xlsx. I have installed survival, xlsx and tlctk2 (i believe tcltk is embedded). When I look at Package Manager i see that although the above packages are installed they are not loaded. I can load survival but when I try to load “xlsx” i get the following error message is: Error: package or namespace load failed for ‘xlsx’: .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so Reason: image not found starting httpd help server … done there may be a couple of hints in here. .onLoad failed in loadNamespace() for 'rJava', details suggests the problem starts with calling rJava. the next line in the error: error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': I have checked this path and see no problems, everything seems to stack up and I find jJava.so where it is supposed to be. However in the next line: dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib I don’t know what the number , 6 after Java.so means but have presumed version number and may be why Java8 is not working. I also note the path …. /JavaVirtualMachines/jdk-11.0.1.jdk/ appears as . /JavaVirtualMachines/1.6.0.jdk/ suggesting a different build the same occurs when I try to load the local source package MH1823 When I try to load HM1823 I get the error message: * installing *source* package ‘mh1823’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error: package or namespace load failed for ‘xlsx’: .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so Reason: image not found Error: package ‘xlsx’ could not be loaded Execution halted ERROR: lazy loading failed for package ‘mh1823’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mh1823’ > I find that the error message is substantially the same suggesting rJava and/or the version of Java. I have tried removing Java 8 from my machine and installing Java 6 but don’t see any difference. It is easy to see that Java 8 has been removed but not easy to see that 6 is installed properly as the path names are still the same. When I try to load either tcltk or tcltk2, my instance of R stops responding entirely. I have also installed Xquartz as I believe this is needed for Mac OS X Can anyone provide some advice on what the issue might be? I have tried reading through the FAQ’s but not found anything to point me in the right direction to correct the problem. Regards, Tom Knox [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
