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 ?
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