Can not install ragp

[missuse]

EDIT: 11.07.2024.
Discussion is about issue reported by MohamedBelal999 in the next comment.

Original issue:
There is quite a bit of small mistakes in https://missuse.github.io/ragp/

check the text carefully and correct.

[MohamedBelal999]

I can not install ragp

[missuse]

Hi MohamedBelal999, can you post what code you used to install ragp and what was the error?

I just checked with:

remotes::install_github("missuse/ragp", force = TRUE)

and it installed without issue on R-4.4.0. Maybe the problem is with personal access token (PAT)? Can you install any R package from github?

[MohamedBelal999]

Hi Milan
When I try to install on R4.4.1 version I have this: (as ‘lib’ is unspecified)

[missuse]

Could you copy and paste the full console output after the installation code ?

[MohamedBelal999]

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Warning: namespace ‘drawProteins’ is not available and has been replaced by .GlobalEnv when processing object ‘p’ [Workspace loaded from ~/.RData] > install.packages("C:/Users/drbel/Desktop/ragp-master.zip", repos = NULL, type = "win.binary") Installing package into ‘C:/Users/drbel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified) > remotes::install_github("missuse/ragp", force = TRUE) Error: Failed to install 'ragp' from GitHub: Timeout was reached: [api.github.com] Resolving timed out after 10008 milliseconds > remotes::install_github("missuse/ragp", force = TRUE) Downloading GitHub repo missuse/ragp@HEAD Downloading Bioconductor repo https://git.bioconductor.org/packages/Biostrings Installing 5 packages: S4Vectors, zlibbioc, IRanges, XVector, GenomeInfoDb Installing packages into ‘C:/Users/drbel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified) Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES' Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘S4Vectors’ ‘zlibbioc’ ‘IRanges’ ‘XVector’ installing the source packages ‘S4Vectors’, ‘zlibbioc’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz' Content type 'application/gzip' length 838187 bytes (818 KB) downloaded 818 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/zlibbioc_1.48.2.tar.gz' Content type 'application/gzip' length 382668 bytes (373 KB) downloaded 373 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz' Content type 'application/gzip' length 481055 bytes (469 KB) downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz' Content type 'application/gzip' length 67825 bytes (66 KB) downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz' Content type 'application/gzip' length 3581806 bytes (3.4 MB) downloaded 3.4 MB * installing *source* package 'S4Vectors' ... ** using staged installation ** libs gcc -I"C:/PROGRA~1/R/R-44~1.1/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AEbufs.c -o AEbufs.o sh: gcc: command not found make: *** [C:/PROGRA~1/R/R-44~1.1/etc/x64/Makeconf:289: AEbufs.o] Error 127 ERROR: compilation failed for package 'S4Vectors' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/S4Vectors' * installing *source* package 'zlibbioc' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs mkdir -p "C:/Users/drbel/AppData/Local/R/win-library/4.4/00LOCK-zlibbioc/00new/zlibbioc/include" "C:/Users/drbel/AppData/Local/R/win-library/4.4/00LOCK-zlibbioc/00new/zlibbioc/libs/x64" make -C zlib-1.2.5 -f"C:/PROGRA~1/R/R-44~1.1/etc/x64/Makeconf" -fwin32/Makefile.gcc libzbioc.a zlib1bioc.dll make[1]: Entering directory '/Users/drbel/AppData/Local/Temp/Rtmpey0V38/R.INSTALL491c3e85e57/zlibbioc/src/zlib-1.2.5' win32/Makefile.gcc:90: warning: overriding recipe for target '.c.o' C:/PROGRA~1/R/R-44~1.1/etc/x64/Makeconf:289: warning: ignoring old recipe for target '.c.o' gcc -m64 -O3 -Wall -DNO_VIZ -DZ_PREFIX -c -o adler32.o adler32.c make[1]: gcc: Command not found make[1]: *** [win32/Makefile.gcc:90: adler32.o] Error 127 make[1]: Leaving directory '/Users/drbel/AppData/Local/Temp/Rtmpey0V38/R.INSTALL491c3e85e57/zlibbioc/src/zlib-1.2.5' make: *** [Makevars.win:7: libzbioc] Error 2 ERROR: compilation failed for package 'zlibbioc' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/zlibbioc' ERROR: dependency 'S4Vectors' is not available for package 'IRanges' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/IRanges' ERROR: dependencies 'S4Vectors', 'IRanges', 'zlibbioc' are not available for package 'XVector' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/XVector' ERROR: dependencies 'S4Vectors', 'IRanges' are not available for package 'GenomeInfoDb' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/GenomeInfoDb' The downloaded source packages are in ‘C:\Users\drbel\AppData\Local\Temp\RtmpsFxUBS\downloaded_packages’ Running `R CMD build`... * checking for file 'C:\Users\drbel\AppData\Local\Temp\RtmpsFxUBS\file7f3069243f55/DESCRIPTION' ... OK * preparing 'Biostrings': * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a 'data/datalist' file should be added * building 'Biostrings_2.72.1.tar.gz' Installing package into ‘C:/Users/drbel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified) ERROR: dependencies 'S4Vectors', 'IRanges', 'XVector', 'GenomeInfoDb' are not available for package 'Biostrings' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/Biostrings' Downloading Bioconductor repo https://git.bioconductor.org/packages/Biostrings Skipping Biostrings, it is already being installed Running `R CMD build`... * checking for file 'C:\Users\drbel\AppData\Local\Temp\RtmpsFxUBS\remotes7f3076f77c55\missuse-ragp-97361fc/DESCRIPTION' ... OK * preparing 'ragp': * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building 'ragp_0.3.5.9000.tar.gz' Installing package into ‘C:/Users/drbel/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified) ERROR: dependency 'Biostrings' is not available for package 'ragp' * removing 'C:/Users/drbel/AppData/Local/R/win-library/4.4/ragp' Warning messages: 1: In missing_devel_warning(pkgdir) : Package Biostrings has compiled code, but no suitable compiler(s) were found. Installation will likely fail. Install Rtools (https://cran.r-project.org/bin/windows/Rtools/).Then use the pkgbuild package, or make sure that Rtools in the PATH. 2: In i.p(...) : installation of package ‘S4Vectors’ had non-zero exit status 3: In i.p(...) : installation of package ‘zlibbioc’ had non-zero exit status 4: In i.p(...) : installation of package ‘IRanges’ had non-zero exit status 5: In i.p(...) : installation of package ‘XVector’ had non-zero exit status 6: In i.p(...) : installation of package ‘GenomeInfoDb’ had non-zero exit status 7: In i.p(...) : installation of package ‘C:/Users/drbel/AppData/Local/Temp/RtmpsFxUBS/file7f304deb775b/Biostrings_2.72.1.tar.gz’ had non-zero exit status 8: In missing_devel_warning(pkgdir) : Package Biostrings has compiled code, but no suitable compiler(s) were found. Installation will likely fail. Install Rtools (https://cran.r-project.org/bin/windows/Rtools/).Then use the pkgbuild package, or make sure that Rtools in the PATH. 9: In i.p(...) : installation of package ‘C:/Users/drbel/AppData/Local/Temp/RtmpsFxUBS/file7f305f5b5db1/ragp_0.3.5.9000.tar.gz’ had non-zero exit status > library("ragp") Error in library("ragp") : there is no package called ‘ragp’ --   > | > >

[missuse]

It seems you are having problems installing packages from Bioconductor, could you try to install Biostrings first and when its completed, install ragp:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

remotes::install_github("missuse/ragp")