[R] Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection

[Bert Gunter]

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.anamarija using 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 using 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 using cri16in002 weight]$ ls
> retina  retina.pos
> [t.cri.asokovic using 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
>
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>
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