Re: [R-pkg-devel] Package fails to build on CRAN Windows server: rtracklayer version too new
Not that it solves your problem per se, but here's what I think CRAN only has rtracklayer 1.48.0 installed on WIndows, i.e. why you get error "namespace 'rtracklayer' 1.48.0 is being loaded, but >= 1.51.5 is required.": * The current Bioconductor "release" is version 3.12 * As you say, Bioconductor 3.12 provides rtracklayer 1.50.0 (https://www.bioconductor.org/packages/3.12/bioc/html/rtracklayer.html) * However, if you look at that page, for Windows it only provides rtracklayer 1.49.5 (this is because rtracklayer never successfully checked on Bioconductor 3.12) * Since the minor version component of rtracklayer 1.49.5 is _odd_, it means it's from a Bioconductor 'devel' branch, i.e. when Bioconductor 3.12 was in devel. * Thus, the most recent Bioconductor "release" where rtracklayer was successfully distributed on Windows is Bioconductor 3.11. * Bioconductor 3.11 provides rtracklayer 1.48.0 (https://www.bioconductor.org/packages/3.11/bioc/html/rtracklayer.html) Clear as mud? I suspect you're using Suggest: rtracklayer (https://github.com/timoast/signac/blob/develop/DESCRIPTION) in your new version. If so, that's good. I also don't think you're doing anything wrong here. Instead, I think it's one of your other Bioconductor dependencies under 'Imports:', or possibly under 'Suggests:', that depend on 'rtracklayer'. The fact that error says "namespace 'rtracklayer' 1.48.0 is being loaded, but >= 1.51.5 is required.", means that one of those Bioconductor dependencies, or their dependencies, has an explicit 'rtracklayer (>= 1.51.5)' under either Depends: or Imports:. My recommendation is that you start identifying that Bioconductor package, and in what way your 'Signac' depends on that package. That will help you decide on what to do next. /Henrik PS. This can happen because Bioconductor allows a package to propagate to a new "release" branch even if it fails on one of the operating systems. On Fri, Apr 16, 2021 at 1:59 PM Tim Stuart wrote: > > Hi all, > > I am trying to submit an update to my package > (https://cran.r-project.org/package=Signac) to CRAN, but it is > currently failing to install on the Windows server. I see the > following installation error: "namespace 'rtracklayer' 1.48.0 is being > loaded, but >= 1.51.5 is required." > > The current release version for rtracklayer is 1.50.0 > (https://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html). > My package does not set a version requirement for rtracklayer, so this > installation error must be caused by having a pre-release version of > one of my bioconductor dependencies installed on the windows server. > > Does anyone know how I might be able to solve this issue? I have tried > contacting the CRAN team a few times by reply-all to the CRAN emails, > but have not had any response from them. This seems like an issue that > could only be solved by fixing the installation of packages on the > CRAN Windows server. > > Incoming test results: > https://win-builder.r-project.org/incoming_pretest/Signac_1.1.2_20210415_225235/ > > Thanks, > Tim > > -- > > This message is for the recipient’s use only, and may contain > confidential, privileged or protected information. Any unauthorized use or > dissemination of this communication is prohibited. If you received this > message in error, please immediately notify the sender and destroy all > copies of this message. The recipient should check this email and any > attachments for the presence of viruses, as we accept no liability for any > damage caused by any virus transmitted by this email. > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] compiling C sources on windows
Thanks Kevin, that fixed the compilation issue. On to the next! Brad On Mon, Apr 19, 2021 at 5:06 PM Kevin Ushey wrote: > I suspect the cause is this: > > > https://github.com/bradleyjeck/epanet2toolkit/blob/aa698568ab85db133f8634928e8cfe661b41ed57/src/epanet2.h#L42-L61 > > Usually, you only need to explicitly use __declspec if you're > compiling with MSVC -- it shouldn't be necessary when using a MinGW > toolchain (as R's toolchain is). You could try adding something like: > > #ifdef __MINGW32__ > #define DLLEXPORT > #endif > > If you need to test locally on Windows, there are free virtual > machines available here: > https://developer.microsoft.com/en-us/microsoft-edge/tools/vms/ > > Best, > Kevin > > On Mon, Apr 19, 2021 at 2:14 AM Brad Eck wrote: > > > > Dear List - > > > > I'm working to get a package of mine that was archived last year back on > to > > CRAN. > > The epanet2toolkit provides an R interface to the EPANET simulation > engine > > that is written in C. > > > > The latest development version of the package builds and checks ok on mac > > and linux but fails to > > compile and install on windows with a bunch of errors like: > > > > undefined reference to `_imp__*` > > > > where * is some function defined in a header file and implemented in the > > corresponding source file. > > > > Am i missing a compiler flag or something? > > > > Current output from winbuilder : > > https://win-builder.r-project.org/9aIcl8Fxu7w1/00install.out > > or https://pastebin.com/8JQNpNKp > > > > source code: https://github.com/bradleyjeck/epanet2toolkit/tree/v22dev > > > > Any insights appreciated. > > > > Brad > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] compiling C sources on windows
I suspect the cause is this: https://github.com/bradleyjeck/epanet2toolkit/blob/aa698568ab85db133f8634928e8cfe661b41ed57/src/epanet2.h#L42-L61 Usually, you only need to explicitly use __declspec if you're compiling with MSVC -- it shouldn't be necessary when using a MinGW toolchain (as R's toolchain is). You could try adding something like: #ifdef __MINGW32__ #define DLLEXPORT #endif If you need to test locally on Windows, there are free virtual machines available here: https://developer.microsoft.com/en-us/microsoft-edge/tools/vms/ Best, Kevin On Mon, Apr 19, 2021 at 2:14 AM Brad Eck wrote: > > Dear List - > > I'm working to get a package of mine that was archived last year back on to > CRAN. > The epanet2toolkit provides an R interface to the EPANET simulation engine > that is written in C. > > The latest development version of the package builds and checks ok on mac > and linux but fails to > compile and install on windows with a bunch of errors like: > > undefined reference to `_imp__*` > > where * is some function defined in a header file and implemented in the > corresponding source file. > > Am i missing a compiler flag or something? > > Current output from winbuilder : > https://win-builder.r-project.org/9aIcl8Fxu7w1/00install.out > or https://pastebin.com/8JQNpNKp > > source code: https://github.com/bradleyjeck/epanet2toolkit/tree/v22dev > > Any insights appreciated. > > Brad > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] compiling C sources on windows
Dear List - I'm working to get a package of mine that was archived last year back on to CRAN. The epanet2toolkit provides an R interface to the EPANET simulation engine that is written in C. The latest development version of the package builds and checks ok on mac and linux but fails to compile and install on windows with a bunch of errors like: undefined reference to `_imp__*` where * is some function defined in a header file and implemented in the corresponding source file. Am i missing a compiler flag or something? Current output from winbuilder : https://win-builder.r-project.org/9aIcl8Fxu7w1/00install.out or https://pastebin.com/8JQNpNKp source code: https://github.com/bradleyjeck/epanet2toolkit/tree/v22dev Any insights appreciated. Brad [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
