In my experience, if I aggressively update my development installation of Bioconductor (including occasional updates of R-devel when appropriate) I can usually replicate most-all failures on the build server which has the same OS as my local machine. It does require aggressive updating though.
On Tue, Nov 6, 2018 at 9:17 AM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > Thanks for the comments. > > A docker image doesn't help with differences between operating systems. > > A docker image wouldn't be practical for the build system, where there are > 1000's of packages installed. > > A docker image would need to be updated daily, since that is what the > build system does; you would need to pull the docker image. > > A docker image with appropriate R and base packages is available; see > https://bioconductor.org/help/docker/ but note that these require that > your own dependencies be installed and kept current. > > Windows builds and tests on 32 and 64 bit platforms, so can take a lot > more time; it is difficult to differentiate between this sort of problem > and timeouts caused by OS-specific or package issues. > > Usually avoidable problems come about because the wrong version of > Bioconductor is in use, or because packages are not current. These can be > checked with > > BiocManager::version() == "3.9" # alternate: BiocManager:::isDevel() > BiocManager::valid() > > In the big picture I hope that we can arrive at a more continuous version > of the builders, but that will not happen soon. > > Martin > > On 11/6/18, 8:37 AM, "Bioc-devel on behalf of 露崎 弘毅" < > bioc-devel-boun...@r-project.org on behalf of k.t.the-ans...@hotmail.co.jp> > wrote: > > Dear Bioc Core Team > > I have created many Bioconductor packages, but it is always hard to > pass the R CMD CHECK/BiocCheck. > > Especially, it is still difficult to construct the identical > environment of single/daily package builder in the local machine. > > Sometimes the error is caused by the difference of the OS (e.g. > Windows ↔︎ Linux, Max), but it is very difficult to trace the reason in the > local machine. > > In the "daily" package builder case, the code can be tested only one > time per day, and it will slow down the package development speed. > > I have often experienced that the BiocCheck in tokay1 (Windows) is > failed due to the CheckTime, but it is difficult to distinguish whether the > error is caused by my source-code or the machine is just busy for the task > of other packages. > > > Why don't you create the docker containers for the single/daily > package builder? > https://www.bioconductor.org/help/docker/ > > I think that it will be very helpful for many BioC developers. > > I want to use the system like below. > > > docker run bioconductor/single_windows > docker run bioconductor/single_linux > docker run bioconductor/single_mac > docker run bioconductor/daily_windows > docker run bioconductor/daily_linux > docker run bioconductor/daily_mac > > > Koki Tsuyuzaki > > [[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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
