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Pandora-IsoMemo / drat

R packages developed in the Pandora IsoMemo project
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install.packages("MpiIsoApp") Issues #3

Closed jroachell15 closed 1 year ago

jroachell15 commented 2 years ago

Download MpiIsoApp package in R

Run these codes in your local R console:

How to start the app:

HOW TO REPORT BUGS:

If you have issues installing the packages, please report your issue here with the package name and what steps you have already done, preferably as descriptive as possible (screenshots, etc.). We will get back to you as soon as we can to solve the issue.

Can please provide:

  • All commands that led to the installation error:
  • The full output of sessionInfo()
  • The output of options("repos")
wahani commented 2 years ago

Can you please provide

jroachell15 commented 2 years ago

@wahani

When trying to install Pandora/IsoMemo Webapp, this error occurred:

The downloaded source packages are in ‘/tmp/RtmpPHJcww/downloaded_packages’ Warning message: In install.packages("MpiIsoApp") : installation of package ‘MpiIsoApp’ had non-zero exit status


sessionInfo()

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Pop!_OS 21.10

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] IsomemoData_1.0.003

loaded via a namespace (and not attached): [1] compiler_4.1.2 tools_4.1.2 curl_4.3.1 jsonlite_1.7.2 modules_0.10.0


options("repos")

$repos CRAN "https://mran.microsoft.com/snapshot/2021-06-01" INWT "https://inwt-vmeh2.inwt.de/r-repo" INWTLab "https://inwtlab.github.io/drat/" PANDORA "https://Pandora-IsoMemo.github.io/drat/"

wahani commented 2 years ago

This is not reproducibly for me. In a fresh R session the installation process works just fine. @jroachell15 I think we have to do a screen sharing session to figure out what is happening.

jroachell15 commented 2 years ago

@wahani

I have successfully installed install.packages("MpiIsoApp"), but the app did not startApplication() correctly and got this error in the app browser

image

Commands leading to the error:

image

sessionInfo():


R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages: [1] shiny_1.6.0 MpiIsoApp_22.02.2 devtools_2.4.1 usethis_2.0.1

loaded via a namespace (and not attached): [1] colorspace_2.0-1 deldir_0.2-10 ellipsis_0.3.2 rsconnect_0.8.18 shinyMatrix_0.6.1 mclust_5.4.7 leaflet_2.0.4.1
[8] rprojroot_2.0.2 fs_1.5.0 rstudioapi_0.13 spatstat.data_2.1-0 remotes_2.3.0 DT_0.18 fansi_0.5.0
[15] mvtnorm_1.1-1 codetools_0.2-18 splines_4.1.3 cachem_1.0.5 knitr_1.33 polyclip_1.10-0 pkgload_1.2.1
[22] jsonlite_1.7.2 spatstat.linnet_2.1-1 spatstat.sparse_2.0-0 readr_1.4.0 compiler_4.1.3 assertthat_0.2.1 RcppZiggurat_0.1.6
[29] Matrix_1.4-0 fastmap_1.1.0 cli_2.5.0 later_1.2.0 htmltools_0.5.1.1 prettyunits_1.1.1 tools_4.1.3
[36] coda_0.19-4 gtable_0.3.0 glue_1.4.2 dplyr_1.0.6 maps_3.3.0 Rcpp_1.0.6 spatstat_2.1-0
[43] jquerylib_0.1.4 cellranger_1.1.0 raster_3.4-10 vctrs_0.3.8 nlme_3.1-155 iterators_1.0.13 crosstalk_1.1.1
[50] xfun_0.23 ps_1.6.0 openxlsx_4.2.3 testthat_3.0.2 mime_0.10 miniUI_0.1.1.1 lifecycle_1.0.0
[57] goftest_1.2-2 MASS_7.3-55 scales_1.1.1 spatstat.core_2.1-2 colourpicker_1.1.0 hms_1.1.0 doSNOW_1.0.19
[64] promises_1.2.0.1 spatstat.utils_2.1-0 parallel_4.1.3 animation_2.6 RColorBrewer_1.1-2 memoise_2.0.0 ggplot2_3.3.3
[71] sass_0.4.0 rpart_4.1.16 stringi_1.6.2 desc_1.3.0 foreach_1.5.1 pkgbuild_1.2.0 zip_2.2.0
[78] geometry_0.4.5 rlang_0.4.11 pkgconfig_2.0.3 lattice_0.20-45 purrr_0.3.4 tensor_1.5 ks_1.13.0
[85] htmlwidgets_1.5.3 Rfast_2.0.3 processx_3.5.2 tidyselect_1.1.1 magrittr_2.0.1 R6_2.5.0 snow_0.4-3
[92] generics_0.1.0 DBI_1.1.1 pillar_1.6.1 withr_2.4.2 mgcv_1.8-39 abind_1.4-5 sp_1.4-5
[99] tibble_3.1.2 crayon_1.4.1 shinyWidgets_0.6.0 KernSmooth_2.23-20 utf8_1.2.1 spatstat.geom_2.1-0 rcarbon_1.4.2
[106] grid_4.1.3 readxl_1.3.1 callr_3.7.0 digest_0.6.27 xtable_1.8-4 httpuv_1.6.1 munsell_0.5.0
[113] bslib_0.2.5.1 shinyjs_2.0.0 magic_1.5-9 sessioninfo_1.1.1 

> options("repos")

$repos CRAN INWT INWTLab "https://mran.microsoft.com/snapshot/2021-06-01" "https://inwt-vmeh2.inwt.de/r-repo" "https://inwtlab.github.io/drat/" PANDORA PANDORA "https://pandora-isomemo.github.io/drat/" "https://pandora-isomemo.github.io/drat/"

jroachell15 commented 2 years ago

@wahani I am retesting all the package installation on my own Windows machine. This bug still remains: https://github.com/Pandora-IsoMemo/drat/issues/3#issuecomment-1074951201

Maybe you can help take a look? thanks!

jroachell15 commented 2 years ago

@wahani FOR MpiIsoApp

I tried the Rtools method of installing:

After I installed Rtools, I proceeded to do the following: options(repos= c(getOption("repos"), PANDORA = "https://pandora-isomemo.github.io/drat/")) install.packages("MpiIsoApp", type="source") startApplication()

RESULT: This bug still remains: https://github.com/Pandora-IsoMemo/drat/issues/3#issuecomment-1074951201

Output Log:

startApplication()


Loading required package: shiny

Listening on http://0.0.0.0:4242 Warning: Error in : lexical error: invalid char in json text. dbsources? (right here) ------^

110: parse_string 109: parseJSON 108: parse_and_simplify 107: fromJSON 106: callAPI 105: getDatabaseList 86: dataExplorerUI 2: runApp 1: startApplication Warning: Error in : lexical error: invalid char in json text. dbsources? (right here) ------^

110: parse_string 109: parseJSON 108: parse_and_simplify 107: fromJSON 106: callAPI 105: getDatabaseList 86: dataExplorerUI 2: runApp 1: startApplication

arunge commented 1 year ago

@jan-abel-inwt I assign you to this ticket. If the wiki is finished, and mentioned issues above are not reproducible, you can close this ticket.

jan-abel-inwt commented 1 year ago

see https://github.com/Pandora-IsoMemo/iso-app/issues/82

content can now be found here: https://github.com/Pandora-IsoMemo/drat/wiki