Hi, thanks for your help, now the package works.
Yesterday among the various attempts I made I ran the function in R in the
image below and from there the package was active and worked correctly.
cordially Pisati Mirko
Il giorno venerdì 13 novembre 2020 alle 01:58:34 UTC+1 Henrik Bengtsson ha
scritto:
> Hi.
>
> The 'sfit' package is special, preventing me from submitting it to
> CRAN without a major rewrite. Because of this, it's not available
> from CRAN and there's no pre-built Windows binary for it either, which
> is what you're running into here.
>
> I basically have to manually build Windows binaries and make them
> available elsewhere, which I've forgotten for a while now. I've made
> one for R 4.0.x available, assuming that's what you're running. I've
> updated
>
> https://github.com/HenrikBengtsson/sfit
>
> with instructions for installing 'sfit', including on Windows.
>
> Let me know if it works,
>
> Henrik
>
> On Thu, Nov 12, 2020 at 12:44 PM Mirko Pisati wrote:
> >
> > Hi ,
> > I have a problem with the process function where it says csC
> > csC <- process (acc, verbose = verbose)
> > print (csC).
> > Failed with error: ‘there is no package called ‘sfit’’
> > I have copy number data of a geo dateset and i want to process it with
> this package. I saw the Vignette page of the package and I followed all the
> setup steps step by step.
> > R gives me the error in which it says it does not find the sfit package,
> if I try to install it from outside with different functions, they all tell
> me that the package is not found or not available for my version of r WHICH
> is 4.0.3 , the last.
> > > source('http://callr.org/install#HenrikBengtsson/sfit')
> > > install.packages("remotes")
> > > remotes::install_github("HenrikBengtsson/sfit")
> > Error in file (filename, "r", encoding = encoding):
> > I can't open this connection
> > Also: Warning message:
> > In file (filename, "r", encoding = encoding):
> > cannot open URL 'http://callr.org/install#HenrikBengtsson/sfit': HTTP
> status was '400 Bad Request'
> > > remotes::install_github("HenrikBengtsson/sfit")
> > Downloading GitHub repo HenrikBengtsson/sfit@HEAD
> > √ checking for file
> 'C:\Users\mirko\AppData\Local\Temp\Rtmp0U19NX\remotes46d42edc29b\HenrikBengtsson-sfit-dd85e19/DESCRIPTION'
>
> (736ms)
> > - preparing 'sfit':
> > √ checking DESCRIPTION meta-information ...
> > - cleaning src
> > - checking for LF line-endings in source and make files and shell
> scripts (637ms)
> > - checking for empty or unneeded directories
> > - building 'sfit_0.3.1.tar.gz'
> >
> > Installing package into ‘C:/Users/mirko/Documents/R/win-library/4.0’
> > (as ‘lib’ is unspecified)
> > * installing *source* package 'sfit' ...
> > ** using staged installation
> > ** libs
> > running 'src/Makefile.win' ...
> > cc -c -o cfit.o cfit.c
> > make: cc: Command not found
> > make: *** [: cfit.o] Error 127
> > ERROR: compilation failed for package 'sfit'
> > * removing 'C:/Users/mirko/Documents/R/win-library/4.0/sfit'
> > Errore: Failed to install 'sfit' from GitHub:
> > (contertito da avviso) installation of package
> ‘C:/Users/mirko/AppData/Local/Temp/Rtmp0U19NX/file46d4153539da/sfit_0.3.1.tar.gz’
>
> had non-zero exit status
> > > sessionInfo()
> > R version 4.0.3 (2020-10-10)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> > Running under: Windows 10 x64 (build 19041)
> >
> > Matrix products: default
> >
> > locale:
> > [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252
> LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C LC_TIME=Italian_Italy.1252
> >
> > attached base packages:
> > [1] parallel stats4 stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.57.0
> Biobase_2.48.0 GenomicRanges_1.40.0
> > [6] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
> BiocGenerics_0.34.0
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_4.0.3 BiocManager_1.30.10 XVector_0.28.0 prettyunits_1.1.1
> R.methodsS3_1.8.1 bitops_1.0-6
> > [7] R.utils_2.10.1 remotes_2.2.0 tools_4.0.3 zlibbioc_1.34.0
> pkgbuild_1.1.0 preprocessCore_1.50.0
> > [13] lattice_0.20-41 Matrix_1.2-18 cli_2.1.0 rstudioapi_0.11 curl_4.3
> GenomeInfoDbData_1.2.3
> > [19] withr_2.3.0 rprojroot_1.3-2 grid_4.0.3 glue_1.4.2 R6_2.4.1
> processx_3.4.4
> > [25] fansi_0.4.1 callr_3.5.1 backports_1.1.10 ps_1.4.0 assertthat_0.2.1
> affy_1.66.0
> > [31] RCurl_1.98-1.2 crayon_1.3.4 affyio_1.58.0 R.oo_1.24.0
> > Please, can someone help me ?
> >
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