Re: [Bioc-devel] [External] different generator for random integers in R-devel

2019-03-19 Thread Tierney, Luke
Use RNGversion("3.5.0") instead. Best, luke On Tue, 19 Mar 2019, Stadler, Michael wrote: > Dear maintainers of the BioC build system > > I have a shy questions regarding R-devel versions on the build machines: > > Currently, these use different versions of R-devel:  > malbec2 | Linux ...   |

Re: [Bioc-devel] Rprintf in a multi-threaded environment

2019-01-29 Thread Tierney, Luke
No functions in the R API are safe to call from any thread other than the R main thread. -- Many may need to allocate from the R heap (more as ALTREP evaolves) and that is not thread safe; -- Many (and with some compilation options nearly all) can signal an error, and the subsequent jump

Re: [Bioc-devel] Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0

2018-12-22 Thread Tierney, Luke
r closures") >> 8: makeUsageCollector(fun, ...) >> 7: collectUsage(fun, enterGlobal = enter) >> 6: findGlobals(value) >> 5: FUN(X[[i]], ...) >> 4: lapply(objs, FUN = function(obj) { >> value = env[[obj]] >> if (is.function(value)) >>

Re: [Bioc-devel] Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0

2018-12-20 Thread Tierney, Luke
N(X[[i]], ...) > 4: lapply(objs, FUN = function(obj) { > value = env[[obj]] > if (is.function(value)) > findGlobals(value) > else character(0) > }) > 3: findLogicalRdir(pkgname, c("T", "F")) > 2: checkCodingPractice(package_di

Re: [Bioc-devel] Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0

2018-12-19 Thread Tierney, Luke
codetools already checks only closures in checkUsageENv and hande checkUsagePackage, so this is anissue on the Bioc side. Best, luke On Tue, 18 Dec 2018, Tierney, Luke wrote: > Codetools should probably be ignoring those. Will have a look > > Sent from my iPhone > >> On Dec

Re: [Bioc-devel] Aliasing `]` breaks BiocCheck::BiocCheck() version 1.18.0

2018-12-18 Thread Tierney, Luke
Codetools should probably be ignoring those. Will have a look Sent from my iPhone > On Dec 18, 2018, at 6:54 AM, Shepherd, Lori > wrote: > > Can you please open an issue for this so we don't lose track of it - > > https://github.com/Bioconductor/BiocCheck/issues > > > > Lori Shepherd > >