Installing orchard issue

Question

Installing orchard issue

anantapantulasa opened this issue 2 years ago · 7 comments

Hi! I tried to install orchaRd using the code from the vignette, but it didn't work. I received the following error.

devtools::install_github("daniel1noble/orchaRd", force = TRUE)
Downloading GitHub repo daniel1noble/orchaRd@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/daniel1noble/orchaRd/tarball/HEAD' failed

Any suggestions for how to fix this issue? I'm using Windows, by the way.

Answer 1 · 2022-08-07T04:42:15.000Z

Hi @anantapantulasa. What version of R are you using? Can you show sessionInfo()? Hard to diagnose as I'm not getting that same error, so I'm not sure if its something with your configuration.

Answer 2 · 2022-08-07T04:57:21.000Z

Also, just a note. Be sure to be connected to the internet before devtools::install("daniel1noble/orchaRd", force = TRUE), this could be related to that error. You need to also have download devtools before running that code

Answer 3 · 2022-08-07T14:30:34.000Z

Hi @daniel1noble, Thanks for your response! I downloaded devtools and connected to the internet before running the code (I did it again, just to make sure); however, I received the same error. Do you think the "tarball/HEAD" is incorrect?
As requested, sessionInfo() information is second block of code below.

install_github("daniel1noble/orchaRd")
Downloading GitHub repo daniel1noble/orchaRd@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/daniel1noble/orchaRd/tarball/HEAD' failed

sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

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

other attached packages:
[1] readr_2.1.2 metafor_3.4-0 metadat_1.2-0 Matrix_1.4-1
[5] forestplot_2.0.1 checkmate_2.1.0 magrittr_2.0.3 dplyr_1.0.9
[9] orchaRd_2.0 reader_1.0.6 NCmisc_1.1.6

loaded via a namespace (and not attached):
[1] mvtnorm_1.1-3 lattice_0.20-45 prettyunits_1.1.1
[4] ps_1.7.1 digest_0.6.29 assertthat_0.2.1
[7] utf8_1.2.2 R6_2.5.1 backports_1.4.1
[10] coda_0.19-4 ggplot2_3.3.6 pillar_1.7.0
[13] rlang_1.0.3 rstudioapi_0.13 callr_3.7.0
[16] mathjaxr_1.6-0 labeling_0.4.2 devtools_2.4.3
[19] stringr_1.4.0 munsell_0.5.0 compiler_4.2.1
[22] vipor_0.4.5 pkgconfig_2.0.3 pkgbuild_1.3.1
[25] ggbeeswarm_0.6.0 tidyselect_1.1.2 tibble_3.1.7
[28] fansi_1.0.3 crayon_1.5.1 tzdb_0.3.0
[31] nlme_3.1-157 xtable_1.8-4 gtable_0.3.0
[34] lifecycle_1.0.1 DBI_1.1.3 pacman_0.5.1
[37] scales_1.2.0 estimability_1.4 cli_3.3.0
[40] stringi_1.7.6 cachem_1.0.6 farver_2.1.1
[43] proftools_0.99-3 fs_1.5.2 remotes_2.4.2
[46] ellipsis_0.3.2 generics_0.1.3 vctrs_0.4.1
[49] latex2exp_0.9.4 tools_4.2.1 glue_1.6.2
[52] beeswarm_0.4.0 purrr_0.3.4 hms_1.1.1
[55] emmeans_1.7.5 processx_3.7.0 pkgload_1.3.0
[58] fastmap_1.1.0 colorspace_2.0-3 sessioninfo_1.2.2
[61] memoise_2.0.1 usethis_2.1.6

Answer 4 · 2022-08-08T00:02:02.000Z

Odd. I’m not entirely sure what the problem is. Sorry. Seems to all work fine on Mac and RHub says Windows too. Can you try to download and install manually: https://kbroman.org/pkg_primer/pages/build.html <https://kbroman.org/pkg_primer/pages/build.html> You should be able to download the file from GitHub and install in your R library. I’m not sure if this will lead to other issues, but for now, it may be a temporary solution. Dan

…

On 8 Aug 2022, at 12:30 am, anantapantulasa ***@***.***> wrote: Hi @daniel1noble <https://github.com/daniel1noble>, Thanks for your response! I downloaded devtools and connected to the internet before running the code (I did it again, just to make sure); however, I received the same error. Do you think the "tarball/HEAD" is incorrect? sessionInfo() information is also below (second block of code).incorrect? install_github("daniel1noble/orchaRd") Downloading GitHub repo ***@***.*** Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/daniel1noble/orchaRd/**tarball/HEAD <https://api.github.com/repos/daniel1noble/orchaRd/**tarball/HEAD>**' failed sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 attached base packages: [1] grid stats graphics grDevices utils datasets [7] methods base other attached packages: [1] readr_2.1.2 metafor_3.4-0 metadat_1.2-0 Matrix_1.4-1 [5] forestplot_2.0.1 checkmate_2.1.0 magrittr_2.0.3 dplyr_1.0.9 [9] orchaRd_2.0 reader_1.0.6 NCmisc_1.1.6 loaded via a namespace (and not attached): [1] mvtnorm_1.1-3 lattice_0.20-45 prettyunits_1.1.1 [4] ps_1.7.1 digest_0.6.29 assertthat_0.2.1 [7] utf8_1.2.2 R6_2.5.1 backports_1.4.1 [10] coda_0.19-4 ggplot2_3.3.6 pillar_1.7.0 [13] rlang_1.0.3 rstudioapi_0.13 callr_3.7.0 [16] mathjaxr_1.6-0 labeling_0.4.2 devtools_2.4.3 [19] stringr_1.4.0 munsell_0.5.0 compiler_4.2.1 [22] vipor_0.4.5 pkgconfig_2.0.3 pkgbuild_1.3.1 [25] ggbeeswarm_0.6.0 tidyselect_1.1.2 tibble_3.1.7 [28] fansi_1.0.3 crayon_1.5.1 tzdb_0.3.0 [31] nlme_3.1-157 xtable_1.8-4 gtable_0.3.0 [34] lifecycle_1.0.1 DBI_1.1.3 pacman_0.5.1 [37] scales_1.2.0 estimability_1.4 cli_3.3.0 [40] stringi_1.7.6 cachem_1.0.6 farver_2.1.1 [43] proftools_0.99-3 fs_1.5.2 remotes_2.4.2 [46] ellipsis_0.3.2 generics_0.1.3 vctrs_0.4.1 [49] latex2exp_0.9.4 tools_4.2.1 glue_1.6.2 [52] beeswarm_0.4.0 purrr_0.3.4 hms_1.1.1 [55] emmeans_1.7.5 processx_3.7.0 pkgload_1.3.0 [58] fastmap_1.1.0 colorspace_2.0-3 sessioninfo_1.2.2 [61] memoise_2.0.1 usethis_2.1.6 — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2X2SUH2LQZ5E62ZUSNV2DVX7CBLANCNFSM55XE5HUQ>. You are receiving this because you were mentioned.

Answer 5 · 2022-08-08T00:03:17.000Z

I also wonder whether this might be an RTools issue. You could install RTools and then try again with devtools:: https://cran.r-project.org/bin/windows/Rtools/ <https://cran.r-project.org/bin/windows/Rtools/> Dan

…

On 8 Aug 2022, at 10:02 am, Daniel Noble ***@***.***> wrote: Odd. I’m not entirely sure what the problem is. Sorry. Seems to all work fine on Mac and RHub says Windows too. Can you try to download and install manually: https://kbroman.org/pkg_primer/pages/build.html <https://kbroman.org/pkg_primer/pages/build.html> You should be able to download the file from GitHub and install in your R library. I’m not sure if this will lead to other issues, but for now, it may be a temporary solution. Dan > On 8 Aug 2022, at 12:30 am, anantapantulasa ***@***.***> wrote: > > > Hi @daniel1noble <https://github.com/daniel1noble>, Thanks for your response! I downloaded devtools and connected to the internet before running the code (I did it again, just to make sure); however, I received the same error. Do you think the "tarball/HEAD" is incorrect? sessionInfo() information is also below (second block of code).incorrect? > > install_github("daniel1noble/orchaRd") > Downloading GitHub repo ***@***.*** > Error in utils::download.file(url, path, method = method, quiet = quiet, : > download from 'https://api.github.com/repos/daniel1noble/orchaRd/**tarball/HEAD <https://api.github.com/repos/daniel1noble/orchaRd/**tarball/HEAD>**' failed > > sessionInfo() > R version 4.2.1 (2022-06-23 ucrt) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 10 x64 (build 22000) > > Matrix products: default > > locale: > [1] LC_COLLATE=English_United States.utf8 > [2] LC_CTYPE=English_United States.utf8 > [3] LC_MONETARY=English_United States.utf8 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.utf8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > [7] methods base > > other attached packages: > [1] readr_2.1.2 metafor_3.4-0 metadat_1.2-0 Matrix_1.4-1 > [5] forestplot_2.0.1 checkmate_2.1.0 magrittr_2.0.3 dplyr_1.0.9 > [9] orchaRd_2.0 reader_1.0.6 NCmisc_1.1.6 > > loaded via a namespace (and not attached): > [1] mvtnorm_1.1-3 lattice_0.20-45 prettyunits_1.1.1 > [4] ps_1.7.1 digest_0.6.29 assertthat_0.2.1 > [7] utf8_1.2.2 R6_2.5.1 backports_1.4.1 > [10] coda_0.19-4 ggplot2_3.3.6 pillar_1.7.0 > [13] rlang_1.0.3 rstudioapi_0.13 callr_3.7.0 > [16] mathjaxr_1.6-0 labeling_0.4.2 devtools_2.4.3 > [19] stringr_1.4.0 munsell_0.5.0 compiler_4.2.1 > [22] vipor_0.4.5 pkgconfig_2.0.3 pkgbuild_1.3.1 > [25] ggbeeswarm_0.6.0 tidyselect_1.1.2 tibble_3.1.7 > [28] fansi_1.0.3 crayon_1.5.1 tzdb_0.3.0 > [31] nlme_3.1-157 xtable_1.8-4 gtable_0.3.0 > [34] lifecycle_1.0.1 DBI_1.1.3 pacman_0.5.1 > [37] scales_1.2.0 estimability_1.4 cli_3.3.0 > [40] stringi_1.7.6 cachem_1.0.6 farver_2.1.1 > [43] proftools_0.99-3 fs_1.5.2 remotes_2.4.2 > [46] ellipsis_0.3.2 generics_0.1.3 vctrs_0.4.1 > [49] latex2exp_0.9.4 tools_4.2.1 glue_1.6.2 > [52] beeswarm_0.4.0 purrr_0.3.4 hms_1.1.1 > [55] emmeans_1.7.5 processx_3.7.0 pkgload_1.3.0 > [58] fastmap_1.1.0 colorspace_2.0-3 sessioninfo_1.2.2 > [61] memoise_2.0.1 usethis_2.1.6 > > — > Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2X2SUH2LQZ5E62ZUSNV2DVX7CBLANCNFSM55XE5HUQ>. > You are receiving this because you were mentioned. > — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2X2SU2P6LUT5TZ665LPNTVYBFAJANCNFSM55XE5HUQ>. You are receiving this because you are subscribed to this thread.

Answer 6 · 2022-08-08T10:44:42.000Z

@anantapantulasa I was thinning about this some more, and I had a closer look. Ok, one possible problem is that emmeans has yet again gone through an update. The problem with the recent update to ver. 1.8.0 is that it requires R 4.2.0>. I see you're running 4.2.1, but you have emmeans a version back. You may also want to try a fresh install of the emmeans package. very 1.8.0 still works perfectly fine with orchaRd (I've done all the testing just today).

Answer 7 · 2022-08-11T01:39:40.000Z

Install issues seem sorted so I'm closing this issue