There is one possible solution posted in http://stackoverflow.com/questions/30610375/how-to-run-permutations-using-mclapply-in-a-reproducible-way-regardless-of-numbe/30627984#30627984 .
As Kasper suggested, it's not a proper way to use set.seed inside a package. I suggest using a parameter for example seed=FALSE to disable the set.seed and if user want the result reproducible, e.g. in demonstration, set seed=TRUE explicitly and set.seed will be run inside the function. Bests, Guangchuang On Wed, Jun 3, 2015 at 8:42 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > For this situation, generate the permutation indexes outside of the > mclapply, and the do mclapply over a list with the indices. > > And btw., please don't use set.seed inside a package; that control should > completely be left to the user. > > Best, > Kasper > > On Wed, Jun 3, 2015 at 7:08 AM, Vincent Carey <st...@channing.harvard.edu> > wrote: > >> This document indicates how to achieve reproducibility independent of the >> underlying physical environment. >> >> http://cran.r-project.org/web/packages/doRNG/vignettes/doRNG.pdf >> >> Let me know if that satisfies the question. >> >> On Wed, Jun 3, 2015 at 5:32 AM, Yu, Guangchuang <g...@connect.hku.hk> >> wrote: >> >> > Der Vincent, >> > >> > RNGkind("L'Ecuyer-CMRG") works as using mc.set.seed=FALSE. >> > >> > When mc.cores changes, the output is not reproducible. >> > >> > I think this issue is also of concern within the Bioconductor community >> as parallel version of permutation test is commonly used now. >> > >> > Best Regards, >> > >> > Guangchuang >> > >> > >> > >> > On Wed, Jun 3, 2015 at 5:17 PM, Vincent Carey < >> st...@channing.harvard.edu> >> > wrote: >> > >> >> Hi, this question belongs on R-help, but perhaps >> >> >> >> >> https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/RngStream.html >> >> >> >> will be useful. >> >> >> >> Best regards >> >> >> >> On Wed, Jun 3, 2015 at 3:11 AM, Yu, Guangchuang <g...@connect.hku.hk> >> >> wrote: >> >> >> >>> Dear all, >> >>> >> >>> I have an issue of setting seed value when using parallel package. >> >>> >> >>> > library("parallel") >> >>> > library("digest") >> >>> > >> >>> > set.seed(0) >> >>> > m <- mclapply(1:10, function(x) sample(1:10), >> >>> + mc.cores=2) >> >>> > digest(m, 'crc32') >> >>> [1] "4827c80c" >> >>> > >> >>> > set.seed(0) >> >>> > m <- mclapply(1:10, function(x) sample(1:10), >> >>> + mc.cores=2) >> >>> > digest(m, 'crc32') >> >>> [1] "e95b9134" >> >>> >> >>> By default, set.seed() will be ignored since mclapply will set the >> seed >> >>> internally. >> >>> >> >>> If we use mc.set.seed=FALSE to disable this feature. It works as >> >>> indicated >> >>> below: >> >>> >> >>> > set.seed(0) >> >>> > m <- mclapply(1:10, function(x) sample(1:10), >> >>> + mc.cores=2, mc.set.seed = FALSE) >> >>> > digest(m, 'crc32') >> >>> [1] "6bbada78" >> >>> > >> >>> > set.seed(0) >> >>> > m <- mclapply(1:10, function(x) sample(1:10), >> >>> + mc.cores=2, mc.set.seed = FALSE) >> >>> > digest(m, 'crc32') >> >>> [1] "6bbada78" >> >>> >> >>> The problems is that the results are also depending on the number of >> >>> cores. >> >>> >> >>> > set.seed(0) >> >>> > m <- mclapply(1:10, function(x) sample(1:10), >> >>> + mc.cores=4, mc.set.seed = FALSE) >> >>> > digest(m, 'crc32') >> >>> [1] "a22e0aab" >> >>> >> >>> >> >>> Any idea? >> >>> >> >>> Best Regards, >> >>> Guangchuang >> >>> -- >> >>> --~--~---------~--~----~------------~-------~--~----~ >> >>> Guangchuang Yu, PhD Candidate >> >>> State Key Laboratory of Emerging Infectious Diseases >> >>> School of Public Health >> >>> The University of Hong Kong >> >>> Hong Kong SAR, China >> >>> www: http://ygc.name >> >>> -~----------~----~----~----~------~----~------~--~--- >> >>> >> >>> [[alternative HTML version deleted]] >> >>> >> >>> _______________________________________________ >> >>> Bioc-devel@r-project.org mailing list >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >>> >> >> >> >> >> > >> > >> > -- >> > --~--~---------~--~----~------------~-------~--~----~ >> > Guangchuang Yu, PhD Candidate >> > State Key Laboratory of Emerging Infectious Diseases >> > School of Public Health >> > The University of Hong Kong >> > Hong Kong SAR, China >> > www: http://ygc.name >> > -~----------~----~----~----~------~----~------~--~--- >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- --~--~---------~--~----~------------~-------~--~----~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: http://ygc.name -~----------~----~----~----~------~----~------~--~--- [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
