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':Â 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)
- Â preparing 'sfit':
√  checking DESCRIPTION meta-information ...
- Â cleaning src
- Â checking for LF line-endings in source and make files and shell scripts (637ms)
- Â checking for empty or unneeded directories
- Â building 'sfit_0.3.1.tar.gz'
 Â
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 Â LC_CTYPE=Italian_Italy.1252 Â Â LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C Â Â Â Â Â Â Â Â Â LC_TIME=Italian_Italy.1252 Â Â
attached base packages:
[1] parallel  stats4   stats   graphics  grDevices utils   datasets  methods  base  Â
other attached packages:
[1] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 Â Â Â Â matrixStats_0.57.0 Â Â Â Â Â Biobase_2.48.0 Â Â Â Â Â Â Â GenomicRanges_1.40.0 Â Â Â
[6] GenomeInfoDb_1.24.2 Â Â Â Â IRanges_2.22.2 Â Â Â Â Â Â Â S4Vectors_0.26.1 Â Â Â Â Â Â BiocGenerics_0.34.0 Â Â Â Â
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     Â
 [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 Â Â Â Â Matrix_1.2-18 Â Â Â Â Â cli_2.1.0 Â Â Â Â Â Â Â rstudioapi_0.11 Â Â Â Â curl_4.3 Â Â Â Â Â Â Â GenomeInfoDbData_1.2.3
[19] withr_2.3.0 Â Â Â Â Â Â rprojroot_1.3-2 Â Â Â Â grid_4.0.3 Â Â Â Â Â Â glue_1.4.2 Â Â Â Â Â Â R6_2.4.1 Â Â Â Â Â Â Â processx_3.4.4 Â Â Â Â
[25] fansi_0.4.1 Â Â Â Â Â Â callr_3.5.1 Â Â Â Â Â Â backports_1.1.10 Â Â Â ps_1.4.0 Â Â Â Â Â Â Â assertthat_0.2.1 Â Â Â affy_1.66.0 Â Â Â Â Â
[31] RCurl_1.98-1.2 Â Â Â Â crayon_1.3.4 Â Â Â Â Â affyio_1.58.0 Â Â Â Â Â R.oo_1.24.0 Â Â Â Â Â
Please, can someone help me ? Â