search

ki-tools / growthstandards

R package for anthropometric growth standard calculations
https://ki-tools.github.io/growthstandards/
MIT License
13 stars 8 forks source link

could not open growthstandards #7

Open Monash-RISE opened 3 years ago

Monash-RISE commented 3 years ago

using Rstudio 1.3.959 and R [Default] [64-bit] C:\Program Files\R\R-4.0.1

when I run remotes::install_github("ki-tools/growthstandards")

I selected "update all". I got this message: Error: Failed to install 'growthstandards' from GitHub: Failed to install 'rbokeh' from GitHub: (converted from warning) package ‘dplyr’ is in use and will not be installed

Any ideas? thanks

hafen commented 3 years ago

Interesting. What happens when you choose "CRAN packages only"?

Monash-RISE commented 3 years ago

thanks for the reply. I tried "CRAN packages only" and got same error:

Installing 21 packages: jsonlite, glue, stringi, withr, pkgbuild, callr, backports, processx, ps, pillar, vctrs, Rcpp, openssl, sys, xfun, knitr, tinytex, isoband, httr, rmarkdown, dplyr Error: Failed to install 'growthstandards' from GitHub: Failed to install 'rbokeh' from GitHub: (converted from warning) package ‘dplyr’ is in use and will not be installed

Any other ideas?

thanks!

On Thu, 1 Oct 2020 at 07:40, Ryan Hafen notifications@github.com wrote:

Interesting. What happens when you choose "CRAN packages only"?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ki-tools/growthstandards/issues/7#issuecomment-701661416, or unsubscribe https://github.com/notifications/unsubscribe-auth/AICYJM3BOXBTGO5Q6KRPSKTSIOQUPANCNFSM4R6QNL2Q .

hafen commented 3 years ago

Try this branch:

remotes::install_github("ki-tools/growthstandards@prepost")

The only difference with this branch is the addition of the INTERGROWTH pre-term postnatal standard and rbokeh dependency removed. It will be merged to master as soon as I add unit tests for the new standard.

Monash-RISE commented 3 years ago

hmmm, still got this: Installing 12 packages: gamlss.dist, dplyr, withr, glue, pkgbuild, callr, backports, processx, ps, pillar, vctrs, isoband Error: Failed to install 'growthstandards' from GitHub: (converted from warning) package ‘dplyr’ is in use and will not be installed

On Thu, 1 Oct 2020 at 08:09, Ryan Hafen notifications@github.com wrote:

Try this branch:

remotes::install_github("ki-tools/growthstandards@prepost")

The only difference with this branch is the addition of the INTERGROWTH pre-term postnatal standard and rbokeh dependency removed. It will be merged to master as soon as I add unit tests for the new standard.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ki-tools/growthstandards/issues/7#issuecomment-701673249, or unsubscribe https://github.com/notifications/unsubscribe-auth/AICYJM4MT65PCARFZEKJ7NTSIOUDDANCNFSM4R6QNL2Q .

hafen commented 3 years ago

Is this from a fresh R session?

If you can share your session info that would be helpful.

Monash-RISE commented 3 years ago

is this what you need? (thanks for your help!!!)

R version 4.0.1 (2020-06-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252

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

other attached packages: [1] janitor_2.0.1 readxl_1.3.1 lubridate_1.7.9 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.1 purrr_0.3.4 readr_1.3.1 tidyr_1.1.1 tibble_3.0.3 [11] ggplot2_3.3.2 tidyverse_1.3.0

loaded via a namespace (and not attached): [1] xfun_0.14 tidyselect_1.1.0 remotes_2.1.1 haven_2.3.1 lattice_0.20-41 snakecase_0.11.0 colorspace_1.4-1 vctrs_0.3.2 generics_0.0.2 [10] htmltools_0.5.0 yaml_2.2.1 blob_1.2.1 rlang_0.4.7 pillar_1.4.4 glue_1.4.1 withr_2.2.0 DBI_1.1.0 dbplyr_1.4.4 [19] modelr_0.1.8 lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.5 evaluate_0.14 knitr_1.28 curl_4.3 [28] fansi_0.4.1 broom_0.5.6 Rcpp_1.0.4.6 scales_1.1.1 backports_1.1.7 jsonlite_1.6.1 fs_1.4.1 hms_0.5.3 digest_0.6.25 [37] stringi_1.4.6 grid_4.0.1 cli_2.0.2 tools_4.0.1 magrittr_1.5 crayon_1.3.4 pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2 [46] reprex_0.3.0 assertthat_0.2.1 rmarkdown_2.2 httr_1.4.1 rstudioapi_0.11 R6_2.4.1 nlme_3.1-148 compiler_4.0.1

On Thu, 1 Oct 2020 at 08:23, Ryan Hafen notifications@github.com wrote:

Is this from a fresh R session?

If you can share your session info that would be helpful.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ki-tools/growthstandards/issues/7#issuecomment-701677957, or unsubscribe https://github.com/notifications/unsubscribe-auth/AICYJM3DJFG3FGI6CMTI3CLSIOVUNANCNFSM4R6QNL2Q .

jessflem commented 3 years ago

Hello, I'm afraid I'm getting a similar error:

Error: Failed to install 'growthstandards' from GitHub: (converted from warning) unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.6: cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.6/PACKAGES'

I've tried installing in the following ways and none have been successful: remotes::install_github("HBGDki/growthstandards") remotes::install_github("ki-tools/growthstandards") remotes::install_github("ki-tools/growthstandards@prepost")

I have restarted R and tried the install updating CRAN packages only.

Thank you very much for your help.

clairewbradley commented 10 months ago

Hi! I am having the same issue and tried all three installation methods. Was there any solution found for this? Thanks so much.

simpar1471 commented 10 months ago

@clairewbradley If using the WHO child growth standards/INTERGROWTH-21st non-fetal standards, the gigs package for R may also be of use to you. (Important conflict of interest statement: I’m the main author for gigs.)

I have managed to install growthstandards myself using the devtools::install_github() function.

hafen commented 8 months ago

I made some updates to the package that should fix this. One is a dependency on rbokeh which is no longer on CRAN. Another is an issue with the custom ggplot geoms provided by the package (not an install issue but a runtime issue). Can you try to reinstall from master and see if it works for you now?