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 <mirko.pis...@gmail.com> 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: *** [<builtin>: 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 ? > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/aroma-affymetrix/082efd76-8546-4708-9ef8-2b7618a64117n%40googlegroups.com. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/aroma-affymetrix/CAFDcVCRnaZaA5Q2yTmhuoRKEJBOawhrYRgfNzi%2B%3D%3D9jGg2fYaw%40mail.gmail.com.
