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. Regards, Tom Knox [[alternative HTML version deleted]]
Since no answer has been forthcoming, my advice is to read the Posting Guide. There is a more appropriate list for your question, and you should take the warning about posting using plain text format on all r-project mailing lists seriously. On September 17, 2019 9:55:31 AM PDT, Thomas Knox <knoxy1827 at gmail.com> 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. > >Regards, > >Tom Knox > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- Sent from my phone. Please excuse my brevity.
On 9/19/19 1:11 AM, Jeff Newmiller wrote:> Since no answer has been forthcoming, my advice is to read the Posting Guide. There is a more appropriate list for your question, and you should take the warning about posting using plain text format on all r-project mailing lists seriously. > > On September 17, 2019 9:55:31 AM PDT, Thomas Knox <knoxy1827 at gmail.com> 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.Which down below we see requires that the java development kit be installed correctly for xlsx. This has been a recurrent issue on the Mac and there are many question about it on the correct mailing list, which is not rhelp, but rather R-SIG-mac. Here's a link to the MarkLogic archive of r-sig-mac https://markmail.org/search/?q=+list%3Aorg.r-project.r-sig-mac+install+java#query:list%3Aorg.r-project.r-sig-mac%20install%20java%20order%3Adate-backward+page:1+state:facets ... and if you don't want to use it then try rseek.org with a search strategy of "install java mac". If that doesn't satisfy, then subscribe and post a question on r-sig-mac with a full description of? results of trying to install a newer version of java. I have version 10.0.1 on my Mojave laptop. -- David.>> 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. >> >> Regards, >> >> Tom Knox >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code.