Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
Hi Nan, Zach, Val, On 12/05/2016 01:45 PM, Obenchain, Valerie wrote: Hi, We need to make several updates to the mac machines. These are the last 2 builders that still need to move from the Hutch to RPCI. Because they are still at the Hutch, access to them is limited. We will get to these updates as soon as we can. Yes, we'll do this soon. However please note that rcdk also fails to pass check on the Mac builder on CRAN because the builder doesn't have Java >= 7 either: https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/rcdk-00check.html As a consequence the version of the Mac binary for rcdk is lagging behind the source package: http://cran.fhcrc.org/web/packages/rcdk/index.html Source package version: 3.3.8 Mac binary version: 3.3.2 Most of the BioC users that are on Mac are not set to install packages from source and need to be able to install binary packages. So even if we update Java on our Mac builders, most Mac users still won't be able to install the latest rcdk and Rcpi. Cheers, H. Valerie On 12/05/2016 01:27 PM, Dan Tenenbaum wrote: Actually it looks like the version of java installed on morelia is 1.6. So it appears that 1.7 (or higher) needs to be installed. Dan - Original Message - From: "Zach Charlop-Powers" To: "Nan Xiao" Cc: "bioc-devel" Sent: Monday, December 5, 2016 1:02:52 PM Subject: Re: [Bioc-devel] Dependency update propagation (rcdk on morelia) Hi Nan, rCDK 3.3.6 requires Java8 and will throw error if the Java environment is incorrect. BioC Build only has Java7 hence the error. The new version of rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on CRAN), these errors should clear up. Please keep me posted if they don't. zach cp On Mon, Dec 5, 2016 at 3:43 PM, Nan Xiao wrote: Hey guys, - it seems this problem is also affecting the other two Bioc packages depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any ideas why? Thanks, -Nan On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: Hi Bioc, - the Rcpi package depends on rcdk, and the rcdk package was updated last week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which removed the Java > 1.8 requirement (previously discussed in https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). I've updated the Rcpi package and specified the rcdk version to be >= 3.3.8, while the most recent Mac build gives the error: ( http://bioconductor.org/checkResults/release/bioc-LATEST/ Rcpi/morelia-buildsrc.html ) namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required. So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8 version requirement is fulfilled by Linux and Windows builds (if I understand correctly). Is there anything I could do to solve this issue? Thanks a lot, -Nan -- http://nanx.me -- http://nanx.me [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
Hi, We need to make several updates to the mac machines. These are the last 2 builders that still need to move from the Hutch to RPCI. Because they are still at the Hutch, access to them is limited. We will get to these updates as soon as we can. Valerie On 12/05/2016 01:27 PM, Dan Tenenbaum wrote: > Actually it looks like the version of java installed on morelia is 1.6. So it > appears that 1.7 (or higher) needs to be installed. > > Dan > > > - Original Message - >> From: "Zach Charlop-Powers" >> To: "Nan Xiao" >> Cc: "bioc-devel" >> Sent: Monday, December 5, 2016 1:02:52 PM >> Subject: Re: [Bioc-devel] Dependency update propagation (rcdk on morelia) >> Hi Nan, >> >> rCDK 3.3.6 requires Java8 and will throw error if the Java environment is >> incorrect. BioC Build only has Java7 hence the error. The new version of >> rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on >> CRAN), these errors should clear up. Please keep me posted if they don't. >> >> zach cp >> >> On Mon, Dec 5, 2016 at 3:43 PM, Nan Xiao wrote: >> >>> Hey guys, >>> >>> - it seems this problem is also affecting the other two Bioc packages >>> depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any >>> ideas why? >>> >>> Thanks, >>> -Nan >>> >>> On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: >>> >>>> Hi Bioc, >>>> >>>> - the Rcpi package depends on rcdk, and the rcdk package was updated last >>>> week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which >>>> removed the Java > 1.8 requirement (previously discussed in >>>> https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). >>>> >>>> I've updated the Rcpi package and specified the rcdk version to be >= >>>> 3.3.8, while the most recent Mac build gives the error: ( >>>> http://bioconductor.org/checkResults/release/bioc-LATEST/ >>>> Rcpi/morelia-buildsrc.html ) >>>> >>>> namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required. >>>> >>>> So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8 >>>> version requirement is fulfilled by Linux and Windows builds (if I >>>> understand correctly). >>>> >>>> Is there anything I could do to solve this issue? >>>> >>>> Thanks a lot, >>>> -Nan >>>> >>>> -- >>>> http://nanx.me >>>> >>> >>> >>> -- >>> http://nanx.me >>> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
Hi Zach and Dan, - thanks a lot for the information, that made things much clearer. >From the build error message, it seems rcdk 3.3.8 only "partially" made to the BioC builds, which means 3.3.8 is available on Linux and Windows, but not Mac (still 3.3.6). Maybe I'll just wait for the Java update (and hope that will propagate the latest rcdk to Mac). Best, -Nan On Mon, Dec 5, 2016 at 4:26 PM, Dan Tenenbaum wrote: > Actually it looks like the version of java installed on morelia is 1.6. So > it appears that 1.7 (or higher) needs to be installed. > > Dan > > > - Original Message - > > From: "Zach Charlop-Powers" > > To: "Nan Xiao" > > Cc: "bioc-devel" > > Sent: Monday, December 5, 2016 1:02:52 PM > > Subject: Re: [Bioc-devel] Dependency update propagation (rcdk on morelia) > > > Hi Nan, > > > > rCDK 3.3.6 requires Java8 and will throw error if the Java environment is > > incorrect. BioC Build only has Java7 hence the error. The new version of > > rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its > on > > CRAN), these errors should clear up. Please keep me posted if they > don't. > > > > zach cp > > > > On Mon, Dec 5, 2016 at 3:43 PM, Nan Xiao wrote: > > > >> Hey guys, > >> > >> - it seems this problem is also affecting the other two Bioc packages > >> depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any > >> ideas why? > >> > >> Thanks, > >> -Nan > >> > >> On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: > >> > >>> Hi Bioc, > >>> > >>> - the Rcpi package depends on rcdk, and the rcdk package was updated > last > >>> week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which > >>> removed the Java > 1.8 requirement (previously discussed in > >>> https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). > >>> > >>> I've updated the Rcpi package and specified the rcdk version to be >= > >>> 3.3.8, while the most recent Mac build gives the error: ( > >>> http://bioconductor.org/checkResults/release/bioc-LATEST/ > >>> Rcpi/morelia-buildsrc.html ) > >>> > >>> namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required. > >>> > >>> So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8 > >>> version requirement is fulfilled by Linux and Windows builds (if I > >>> understand correctly). > >>> > >>> Is there anything I could do to solve this issue? > >>> > >>> Thanks a lot, > >>> -Nan > >>> > >>> -- > >>> http://nanx.me > >>> > >> > >> > >> > >> -- > >> http://nanx.me > >> > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- http://nanx.me [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
Actually it looks like the version of java installed on morelia is 1.6. So it appears that 1.7 (or higher) needs to be installed. Dan - Original Message - > From: "Zach Charlop-Powers" > To: "Nan Xiao" > Cc: "bioc-devel" > Sent: Monday, December 5, 2016 1:02:52 PM > Subject: Re: [Bioc-devel] Dependency update propagation (rcdk on morelia) > Hi Nan, > > rCDK 3.3.6 requires Java8 and will throw error if the Java environment is > incorrect. BioC Build only has Java7 hence the error. The new version of > rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on > CRAN), these errors should clear up. Please keep me posted if they don't. > > zach cp > > On Mon, Dec 5, 2016 at 3:43 PM, Nan Xiao wrote: > >> Hey guys, >> >> - it seems this problem is also affecting the other two Bioc packages >> depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any >> ideas why? >> >> Thanks, >> -Nan >> >> On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: >> >>> Hi Bioc, >>> >>> - the Rcpi package depends on rcdk, and the rcdk package was updated last >>> week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which >>> removed the Java > 1.8 requirement (previously discussed in >>> https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). >>> >>> I've updated the Rcpi package and specified the rcdk version to be >= >>> 3.3.8, while the most recent Mac build gives the error: ( >>> http://bioconductor.org/checkResults/release/bioc-LATEST/ >>> Rcpi/morelia-buildsrc.html ) >>> >>> namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required. >>> >>> So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8 >>> version requirement is fulfilled by Linux and Windows builds (if I >>> understand correctly). >>> >>> Is there anything I could do to solve this issue? >>> >>> Thanks a lot, >>> -Nan >>> >>> -- >>> http://nanx.me >>> >> >> >> >> -- >> http://nanx.me >> > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
Hi Nan, rCDK 3.3.6 requires Java8 and will throw error if the Java environment is incorrect. BioC Build only has Java7 hence the error. The new version of rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on CRAN), these errors should clear up. Please keep me posted if they don't. zach cp On Mon, Dec 5, 2016 at 3:43 PM, Nan Xiao wrote: > Hey guys, > > - it seems this problem is also affecting the other two Bioc packages > depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any > ideas why? > > Thanks, > -Nan > > On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: > >> Hi Bioc, >> >> - the Rcpi package depends on rcdk, and the rcdk package was updated last >> week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which >> removed the Java > 1.8 requirement (previously discussed in >> https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). >> >> I've updated the Rcpi package and specified the rcdk version to be >= >> 3.3.8, while the most recent Mac build gives the error: ( >> http://bioconductor.org/checkResults/release/bioc-LATEST/ >> Rcpi/morelia-buildsrc.html ) >> >> namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required. >> >> So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8 >> version requirement is fulfilled by Linux and Windows builds (if I >> understand correctly). >> >> Is there anything I could do to solve this issue? >> >> Thanks a lot, >> -Nan >> >> -- >> http://nanx.me >> > > > > -- > http://nanx.me > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
Hey guys, - it seems this problem is also affecting the other two Bioc packages depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any ideas why? Thanks, -Nan On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: > Hi Bioc, > > - the Rcpi package depends on rcdk, and the rcdk package was updated last > week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which > removed the Java > 1.8 requirement (previously discussed in > https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). > > I've updated the Rcpi package and specified the rcdk version to be >= > 3.3.8, while the most recent Mac build gives the error: ( > http://bioconductor.org/checkResults/release/bioc- > LATEST/Rcpi/morelia-buildsrc.html ) > > namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required. > > So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8 version > requirement is fulfilled by Linux and Windows builds (if I understand > correctly). > > Is there anything I could do to solve this issue? > > Thanks a lot, > -Nan > > -- > http://nanx.me > -- http://nanx.me [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel