Problem with Instalation

[Maryam-Sayadi]

Hi,

I do get the following error message while trying to install :

ERROR: dependency ‘gChain’ is not available for package ‘gGnome’

Could you please advise? I am using R version 3.6.2.

Thanks,

[ShaiberAlon]

Hi @Maryam-Sayadi ,

can you try manually installing gChain before trying to install gGnome again?

run:
devtools::instal_github(‘mskilab/gChain’)

[W-L-W]

I'm pretty new to R but think I managed to get gGnome working after working my way through the dependency error messages - I ran:
devtools::install_github('mskilab/bamUtils')
devtools::install_github('mskilab/gChain')
devtools::install_github('mskilab/gGnome')

and finally I needed
install.packages('ellipsis')
before I could run
library(gGnome)

Hope this might be helpful.

[jayeung12]

Hi,

I also get error messages when trying to install:

The same issue happens when I try to use:
foldername = "C:/Users/user/Documents/R/win-library/4.1/"
install.packages('C:/Users/user/Downloads/gGnome-1.0.tar.gz', lib=foldername,dependencies=TRUE,repos = NULL)

If I try to install from the gGnome-1.0.zip file, I get the following issue:
library("gGnome", lib.loc = "C:/Users/user/Documents/R/win-library/4.1/")
Error in library("gGnome", lib.loc = "C:/Users/user/Documents/R/win-library/4.1/") :
‘gGnome’ is not a valid installed package

I have tried this with R version 3.6 and 4.1 on two separate computers with the same results

Here is my session info:

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 BiocManager_1.30.20 urlchecker_1.0.1 pillar_1.8.1
[5] compiler_4.1.2 later_1.3.0 remotes_2.4.2 profvis_0.3.7
[9] prettyunits_1.1.1 tools_4.1.2 digest_0.6.31 pkgbuild_1.4.0
[13] pkgload_1.3.2 memoise_2.0.1 lifecycle_1.0.3 tibble_3.1.8
[17] pkgconfig_2.0.3 rlang_1.0.6 shiny_1.7.4 cli_3.6.0
[21] rstudioapi_0.14 curl_5.0.0 xfun_0.37 fastmap_1.1.1
[25] knitr_1.42 withr_2.5.0 stringr_1.5.0 dplyr_1.1.0
[29] desc_1.4.2 htmlwidgets_1.6.1 generics_0.1.3 fs_1.6.1
[33] vctrs_0.5.2 devtools_2.4.5 rprojroot_2.0.3 tidyselect_1.2.0
[37] glue_1.6.2 R6_2.5.1 processx_3.8.0 fansi_1.0.4
[41] sessioninfo_1.2.2 purrr_1.0.1 callr_3.7.3 magrittr_2.0.3
[45] codetools_0.2-18 usethis_2.1.6 promises_1.2.0.1 ps_1.7.2
[49] ellipsis_0.3.2 htmltools_0.5.4 mime_0.12 xtable_1.8-4
[53] httpuv_1.6.6 utf8_1.2.3 stringi_1.7.12 miniUI_0.1.1.1
[57] cachem_1.0.7 crayon_1.5.2

Appreciate any help,
Jason

[imielinski]

Have you tried using devtools::install_github as in the instructions? Also we have unfortunately not tested gGnome on Windows (only linux and macosx), so cannot make any guarantees that it will work. Marcin Hi, I also get error messages when trying to install: The same issue happens when I try to use: foldername = "C:/Users/user/Documents/R/win-library/4.1/" install.packages('C:/Users/user/Downloads/gGnome-1.0.tar.gz', lib=foldername,dependencies=TRUE,repos = NULL) If I try to install from the gGnome-1.0.zip file, I get the following issue: library("gGnome", lib.loc = "C:/Users/user/Documents/R/win-library/4.1/") Error in library("gGnome", lib.loc = "C:/Users/user/Documents/R/win-library/4.1/") : ‘gGnome’ is not a valid installed package I have tried this with R version 3.6 and 4.1 on two separate computers with the same results Here is my session info: sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] Rcpp_1.0.10 BiocManager_1.30.20 urlchecker_1.0.1 pillar_1.8.1 [5] compiler_4.1.2 later_1.3.0 remotes_2.4.2 profvis_0.3.7 [9] prettyunits_1.1.1 tools_4.1.2 digest_0.6.31 pkgbuild_1.4.0 [13] pkgload_1.3.2 memoise_2.0.1 lifecycle_1.0.3 tibble_3.1.8 [17] pkgconfig_2.0.3 rlang_1.0.6 shiny_1.7.4 cli_3.6.0 [21] rstudioapi_0.14 curl_5.0.0 xfun_0.37 fastmap_1.1.1 [25] knitr_1.42 withr_2.5.0 stringr_1.5.0 dplyr_1.1.0 [29] desc_1.4.2 htmlwidgets_1.6.1 generics_0.1.3 fs_1.6.1 [33] vctrs_0.5.2 devtools_2.4.5 rprojroot_2.0.3 tidyselect_1.2.0 [37] glue_1.6.2 R6_2.5.1 processx_3.8.0 fansi_1.0.4 [41] sessioninfo_1.2.2 purrr_1.0.1 callr_3.7.3 magrittr_2.0.3 [45] codetools_0.2-18 usethis_2.1.6 promises_1.2.0.1 ps_1.7.2 [49] ellipsis_0.3.2 htmltools_0.5.4 mime_0.12 xtable_1.8-4 [53] httpuv_1.6.6 utf8_1.2.3 stringi_1.7.12 miniUI_0.1.1.1 [57] cachem_1.0.7 crayon_1.5.2 Appreciate any help, Jason — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[jayeung12]

Thank you for your reply - yes, that leads to the error message in the .png after installing all dependencies. I will attempt installation on those other systems instead

Jason