[Bioc-devel] Installing libsbml for rsbml on a mac?
The INSTALL file for rsbml says ~/b/git/rsbml master$ cat INSTALL ... To build rsbml on the Mac, first install libsbml with: `brew install homebrew/science/libsbml`. but ~/b/git/rsbml master$ brew install homebrew/science/libsbml Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated. If I download and build from source curl -O https://s3.amazonaws.com/linux-provisioning/libSBML-5.10.2-core-src.tar.gz tar xzf libSBML-5.10.2-core-src.tar.gz ./configure --enable-layout make make install when I install rsbml things go well enough until ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘rsbml’: .onLoad failed in loadNamespace() for 'rsbml', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/ma38727/Library/Caches/pkgserver/library/78c7d37adb9cb6df9d8f1ec10fed882b/00LOCK-rsbml/00new/rsbml/libs/rsbml.so': dlopen(/Users/ma38727/Library/Caches/pkgserver/library/78c7d37adb9cb6df9d8f1ec10fed882b/00LOCK-rsbml/00new/rsbml/libs/rsbml.so, 6): Symbol not found: _ASTNode_isName Referenced from: /usr/local/lib/libsbml.5.dylib Expected in: flat namespace in /usr/local/lib/libsbml.5.dylib Error: loading failed Execution halted Any hints? Thanks, Martin ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] How can I maintain a stable list of source urls
I was talking with another nix user a while back about this problem, and I don't think there's a good solution at the moment. One thing that strikes me is that when release packages get updated the old versions get put in an archive and the source tarball remains available e.g. https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/biomaRt/ Currently this archive is only created if a package is updated during the release cycle. Would it be sufficient for all packages to get an archive URL as default? Then if they aren't updated during a release cycle that URL is fine, and if there are updates you get a new link to the new package source. Something I'm not clear about is when you say this could be affected by "changes inside the repo that affect the hash output". AFAIK a new tarball will only propagate to the download page if the version number has been bumped, and so a new link will be generated. I'm not sure how it's possible to get a tarball with the same name but a different hash. On Tue, 31 Mar 2020 at 23:03, Tim Sears wrote: > Hi > I am working to make bioconductor packages available through the nix > package manager (https://nixos.org/). Currently nixpkgs points to a source > url on one of the bioconductor mirrors. nixpkgs tracks the url and a sha256 > hash of the unpacked source link. Unfortunately the links themselves often > disappear as the packages get updated either due to a version number change > or changes inside the repo that affect the hash output. This breaks > corresponding nix package. This happens even for stable bioconductor > versions like 3.10. nixpkgs aims for reproducible builds, which means when > things change, the url should reflect the change too and the contents > behich old urls should be preserved long enough to manage the change. Do > you have any suggestions short of rebuilding a bioconductor mirror with > immutable urls? > > Thanks, > TIm > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Last Day to Submit New Packages for Bioconductor Release 3.11
The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.11 release is TODAY 5 PM EST! Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be accepted by Wednesday April 22nd. Submit new packages at https://github.com/Bioconductor/Contributions Submissions after Today and those that are not accepted by April 22nd will still be able to be in Bioconductor but will be included in the development branch until the 3.12 release in Fall. Please do not expect rush reviews or exceptions; reviews of packages submitted after today Friday April 3rd will be time-dependent of the reviewer based on other pre-release preparation. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Contributed annotations deadline
Hello Bioconductor community! The deadline for any community contributed annotation packages is April 22nd. Please submit these packages to me by then. Thank you, Kayla E. Interdonato, MS Programmer/Analyst Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics (716)845-1300 x4621 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Installing libsbml for rsbml on a mac?
Does this work for you? https://github.com/mythosil/homebrew-libsbml Michael On Fri, Apr 3, 2020 at 2:20 AM Martin Morgan wrote: > The INSTALL file for rsbml says > > ~/b/git/rsbml master$ cat INSTALL > ... > > To build rsbml on the Mac, first install libsbml with: > `brew install homebrew/science/libsbml`. > > but > > ~/b/git/rsbml master$ brew install homebrew/science/libsbml > Error: homebrew/science was deprecated. This tap is now empty as all its > formulae were > migrated. > > If I download and build from source > > curl -O > https://s3.amazonaws.com/linux-provisioning/libSBML-5.10.2-core-src.tar.gz > tar xzf libSBML-5.10.2-core-src.tar.gz > ./configure --enable-layout > make > make install > > when I install rsbml things go well enough until > > ** testing if installed package can be loaded from temporary location > Error: package or namespace load failed for ‘rsbml’: >.onLoad failed in loadNamespace() for 'rsbml', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > > '/Users/ma38727/Library/Caches/pkgserver/library/78c7d37adb9cb6df9d8f1ec10fed882b/00LOCK-rsbml/00new/rsbml/libs/rsbml.so': > > dlopen(/Users/ma38727/Library/Caches/pkgserver/library/78c7d37adb9cb6df9d8f1ec10fed882b/00LOCK-rsbml/00new/rsbml/libs/rsbml.so, > 6): Symbol not found: _ASTNode_isName > Referenced from: /usr/local/lib/libsbml.5.dylib > Expected in: flat namespace > in /usr/local/lib/libsbml.5.dylib > Error: loading failed > Execution halted > > Any hints? > > Thanks, Martin > -- Michael Lawrence Senior Scientist, Bioinformatics and Computational Biology Genentech, A Member of the Roche Group Office +1 (650) 225-7760 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] R Dependency Warning
Hello, I'm in the process of submitting two packages to Bioconductor, MOMA and its associated data package moma.gbmexample. I keep getting this warning about the R dependency: * Checking R Version dependency... * WARNING: Unless package includes compressed data, remove R version dependency Both packages do have compressed data and I have tried both making the dependency 4.0.0 and 3.6 but have gotten the error both times. Which is the correct R version to list as the dependency on the upcoming release version? Or is this a warning that should be ignored given that I do have compressed data? Thank you Sunny Jones [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R Dependency Warning
If you have compressed data it can be ignored. 4.0.0 is what the package would be released under so I recommend that. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Sunny Jones Sent: Friday, April 3, 2020 2:13 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] R Dependency Warning Hello, I'm in the process of submitting two packages to Bioconductor, MOMA and its associated data package moma.gbmexample. I keep getting this warning about the R dependency: * Checking R Version dependency... * WARNING: Unless package includes compressed data, remove R version dependency Both packages do have compressed data and I have tried both making the dependency 4.0.0 and 3.6 but have gotten the error both times. Which is the correct R version to list as the dependency on the upcoming release version? Or is this a warning that should be ignored given that I do have compressed data? Thank you Sunny Jones [[alternative HTML version deleted]] ___ 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R Dependency Warning
Hi Sunny, I would venture a guess and suggest that is about the too fined grained version you defined in the DESCRIPTION file. I would suggest, that you try to define an R version, which follows the format x.y and not x.y.z. So for you that would be R (>= 4.0). Hope that works, Felix -Ursprüngliche Nachricht- Von: Bioc-devel Im Auftrag von Sunny Jones Gesendet: Freitag, 3. April 2020 20:14 An: bioc-devel@r-project.org Betreff: [Bioc-devel] R Dependency Warning Hello, I'm in the process of submitting two packages to Bioconductor, MOMA and its associated data package moma.gbmexample. I keep getting this warning about the R dependency: * Checking R Version dependency... * WARNING: Unless package includes compressed data, remove R version dependency Both packages do have compressed data and I have tried both making the dependency 4.0.0 and 3.6 but have gotten the error both times. Which is the correct R version to list as the dependency on the upcoming release version? Or is this a warning that should be ignored given that I do have compressed data? Thank you Sunny Jones [[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] R Dependency Warning
it's a warning and you should ignore it. We will try to improve the check. Martin On 4/3/20, 2:14 PM, "Bioc-devel on behalf of Sunny Jones" wrote: Hello, I'm in the process of submitting two packages to Bioconductor, MOMA and its associated data package moma.gbmexample. I keep getting this warning about the R dependency: * Checking R Version dependency... * WARNING: Unless package includes compressed data, remove R version dependency Both packages do have compressed data and I have tried both making the dependency 4.0.0 and 3.6 but have gotten the error both times. Which is the correct R version to list as the dependency on the upcoming release version? Or is this a warning that should be ignored given that I do have compressed data? Thank you Sunny Jones [[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] R Dependency Warning
Thanks all! Changing to 4.0 still produced the warning but I'll ignore it as was recommended. Sunny On Fri, Apr 3, 2020 at 2:20 PM Felix Ernst wrote: > Hi Sunny, > > I would venture a guess and suggest that is about the too fined grained > version you defined in the DESCRIPTION file. > > I would suggest, that you try to define an R version, which follows the > format x.y and not x.y.z. So for you that would be R (>= 4.0). > > Hope that works, > > Felix > > -Ursprüngliche Nachricht- > Von: Bioc-devel Im Auftrag von Sunny > Jones > Gesendet: Freitag, 3. April 2020 20:14 > An: bioc-devel@r-project.org > Betreff: [Bioc-devel] R Dependency Warning > > Hello, > > I'm in the process of submitting two packages to Bioconductor, MOMA and > its associated data package moma.gbmexample. I keep getting this warning > about the R dependency: > > * Checking R Version dependency... > * WARNING: Unless package includes compressed data, remove R > version dependency > > Both packages do have compressed data and I have tried both making the > dependency 4.0.0 and 3.6 but have gotten the error both times. Which is the > correct R version to list as the dependency on the upcoming release > version? Or is this a warning that should be ignored given that I do have > compressed data? > > Thank you > Sunny Jones > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
