This is often related to permissions' issues on your local machine, for which you provided none of the (requested) info. If so, this is not an R issue. See ?sessioninfo.
Also, this is a plain text list. Don't post in html, as it can make code unreadable. Cheers, Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, Jul 9, 2019 at 8:31 AM Ana Marija <sokovic.anamar...@gmail.com> wrote: > Hello, > > I am trying to run this program FUSION.assoc_test.R from : > http://gusevlab.org/projects/fusion/#typical-analysis-and-output > > [t.cri.asokovic@cri16in002 fusion_twas-master]$ Rscript > FUSION.assoc_test.R > \ > > --sumstats /gpfs/data/stranger-lab/anamaria/meta_gwas/META_CHR22_1.txt \ > > --weights ./weight/retina.pos \ > > --weights_dir ./weight/ \ > > --ref_ld_chr ./LDREF/1000G.EUR.22 \ > > --chr 22 \ > > --out PGC2.SCZ.22.dat > Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection > Calls: load -> readChar > In addition: Warning message: > In readChar(con, 5L, useBytes = TRUE) : > cannot open compressed file './weight//NA', probable reason 'No such file > or directory' > Execution halted > > I also formatted my retina.pos to be the same as in the given example (the > example does run for me) > > WGT ID CHR P0 P1 > retina/retina.ENSG00000000419.wgt.RDat DPM1 chr20 50934867 > 50958555 > retina/retina.ENSG00000000457.wgt.RDat SCYL3 chr1 169849631 > 169894267 > retina/retina.ENSG00000000460.wgt.RDat C1orf112 chr1 169662007 > 169854080 > retina/retina.ENSG00000000938.wgt.RDat FGR chr1 27612064 > 27635277 > retina/retina.ENSG00000000971.wgt.RDat CFH chr1 196651878 > 196747504 > > > [t.cri.asokovic@cri16in002 weight]$ ls > retina retina.pos > [t.cri.asokovic@cri16in002 weight]$ pwd > /gpfs/data/stranger-lab/anamaria/fusion/fusion_twas-master/weight > > in retina folder I have all .RDat files > > Does anyone know what is the issue here? It is impossible to get an answer > from the developer. > > Thanks > Ana > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
