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(This issue was resolved!)Patient level prediction - build R package fails!

patientprediction

#1

Dear all,

I have downloaded an R package from an ATLAS platform.
I made all changes which were mentioned in the “readme.md” (step1: step5).
I push it into my github and ran: devtools::install_github(“gitUsername/NameOf Package”,dependencies = FALSE).

It generated the following error:

Error: Failed to install ‘TreatedRightAwayAndDeath’ from GitHub:
(converted from warning) installation of package ‘/tmp/RtmpP3U27z/file5b432a5210d3/TreatedRightAwayAndDeath_0.0.1.tar.gz’ had non-zero exit status
Traceback:

  1. devtools::install_github(“nzkermani/TreatedRightAwayAndDeath”,
    . dependencies = FALSE)
  2. pkgbuild::with_build_tools({
    . ellipsis::check_dots_used(action = getOption(“devtools.ellipsis_action”,
    . rlang::warn))
    . {
    . remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir,
    . auth_token = auth_token, host = host)
    . install_remotes(remotes, auth_token = auth_token, host = host,
    . dependencies = dependencies, upgrade = upgrade, force = force,
    . quiet = quiet, build = build, build_opts = build_opts,
    . build_manual = build_manual, build_vignettes = build_vignettes,
    . repos = repos, type = type, …)
    . }
    . }, required = FALSE)
  3. install_remotes(remotes, auth_token = auth_token, host = host,
    . dependencies = dependencies, upgrade = upgrade, force = force,
    . quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual,
    . build_vignettes = build_vignettes, repos = repos, type = type,
    . …)
  4. tryCatch(res[[i]] <- install_remote(remotes[[i]], …), error = function(e) {
    . stop(remote_install_error(remotes[[i]], e))
    . })
  5. tryCatchList(expr, classes, parentenv, handlers)
  6. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. value[3L]

I appreciate your help!

These are my setting and R version etc.

R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/jovyan/.conda/lib/libopenblasp-r0.3.12.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages:
[1] gdtools_0.2.2 OhdsiSharing_0.2.2

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 pillar_1.5.0 compiler_4.0.3
[4] prettyunits_1.1.1 base64enc_0.1-3 remotes_2.2.0
[7] tools_4.0.3 getPass_0.2-2 testthat_3.0.2.9000
[10] digest_0.6.27 pkgbuild_1.2.0 uuid_0.1-4
[13] pkgload_1.2.0 jsonlite_1.7.2 evaluate_0.14
[16] memoise_2.0.0 lifecycle_1.0.0 rlang_0.4.10
[19] IRdisplay_1.0 cli_2.3.1 curl_4.3
[22] IRkernel_1.1.1 fastmap_1.1.0 rJava_0.9-13
[25] repr_1.1.3 withr_2.4.1 systemfonts_1.0.1
[28] fs_1.5.0 desc_1.2.0 devtools_2.3.2
[31] rprojroot_2.0.2 glue_1.4.2 R6_2.5.0
[34] processx_3.4.5 fansi_0.4.2 sessioninfo_1.1.1
[37] pbdZMQ_0.3-5 callr_3.5.1 magrittr_2.0.1
[40] usethis_1.6.3 ps_1.6.0 ellipsis_0.3.1
[43] htmltools_0.5.1.1 assertthat_0.2.1 utf8_1.1.4
[46] cachem_1.0.4 crayon_1.4.1

Bests,
Nazanin

This issue was resolved!


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