Error when launching Shiny app in package sangeranalyseR #60
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I also get this error, I typed
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Hi, I'm the original poster. |
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I just realised that there are some errors in Shiny applications because some imported R packages worked differently in R 4.0 (like the graphs and sequences don't appear in the Shiny apps). Would you please try R 3.6 to see whether you can run the Shiny app command ? I will fix the dependency issue and find a Windows computer to test sangeranalyseR recently. Sorry for my late reply. Howard |
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I have updated the R package in the latest commit. Please check whether the graphs and results appear in Shiny apps ( @bomsterr Could you run with your data again to see whether you can launch the app now? Thanks a lot. cheers, Howard |
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Hi Howard, I ran Warning: Error in value[[3L]]: Couldn't normalize path in |
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Hi Howard, I also got the same error. |
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Hi, Howard,
Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): |
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Hi Howard, I have also the same problem when I try to launch Shiny app using launchApp(my_aligned_contigs)
Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): Cheers, |
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Hi @bomsterr, @AlexGaithuma, @SilonovSA, @Virginia-b, Sorry for the late reply.
Here is the way to install sangeranalyseR with the latest version. Thanks! Howard |
I have a similar issue. |
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Hi, I have the same problem. I am new, I was trying with the ones suggested in the previous comments but it was not possible. She left the error message. An error has occurred! And this corresponds to my data.
Stay tuned, thanks <3 |
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@Kuanhao-Chao I'm facing the same problem |
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I also have this same problem on Mac. |
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Hi, I had the same problem, but was able to resolve it by deleting the project and creating an entirely new project with a new environment (make sure to click use renv with this project when in Rstudio). I assume it was some sort of conflict with one of the other packages or package versions I was using. Anyway, reinstalling all packages seemed to do the trick. The only things I did after opening the project were to create an R notebook (installing R-markdown dependencies in the process), then run the following code to install the package, followed by the reproducible example. SummaryThe following document is following the introduction manual given here: https://sangeranalyser.readthedocs.io/en/latest/index.html Install scriptInstall Development versionReproducible ExampleHere is session info in case anyone wants to try to puzzle out what was causing the issue: |
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Thank you for sharing how you resolved the issue!
…On Fri, Aug 9, 2024 at 10:58 AM JaredSipesBioE ***@***.***> wrote:
Hi, I had the same problem, but was able to resolve it by deleting the
project and creating an entirely new project with a new environment (*make
sure to click use renv with this project* when in Rstudio). I assume it
was some sort of conflict with one of the other packages or package
versions I was using. Anyway, reinstalling all packages seemed to do the
trick.
The only things I did after opening the project were to create an R
notebook (installing R-markdown dependencies in the process), then run the
following code to install the package, followed by the reproducible example.
Summary
The following document is following the introduction manual given here:
https://sangeranalyser.readthedocs.io/en/latest/index.html
Install script
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("sangeranalyseR")
Install Development version
install.packages("devtools")
library(devtools)
## Install the release version
install_github("roblanf/sangeranalyseR", ref = "master")
## Install the development version
install_github("roblanf/sangeranalyseR", ref = "develop")
library(sangeranalyseR)
Reproducible Example
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
ACHLO_contigs <- SangerAlignment(ABIF_Directory = parentDir,
REGEX_SuffixForward = "_[0-9]*_F.ab1$",
REGEX_SuffixReverse = "_[0-9]*_R.ab1$")
launchApp(ACHLO_contigs)
Here is session info in case anyone wants to try to puzzle out what was
causing the issue:
sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] tools parallel stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] sangeranalyseR_1.13.0 logger_0.3.0 BiocStyle_2.33.1 seqinr_4.2-36 knitr_1.48 rmarkdown_2.27
[7] openxlsx_4.2.6.1 shinyWidgets_0.8.6 ggdendro_0.2.0 shinycssloaders_1.1.0 excelR_0.4.0 zeallot_0.1.0
[13] DT_0.33 plotly_4.10.4 ggplot2_3.5.1 data.table_1.15.4 shinyjs_2.1.0 shinydashboard_0.7.2
[19] shiny_1.9.1 gridExtra_2.3 sangerseqR_1.41.0 pwalign_1.1.0 reshape2_1.4.4 DECIPHER_3.1.4
[25] Biostrings_2.73.1 GenomeInfoDb_1.41.1 XVector_0.45.0 IRanges_2.39.2 S4Vectors_0.43.2 BiocGenerics_0.51.0
[31] ape_5.8 stringr_1.5.1 devtools_2.4.5 usethis_3.0.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 remotes_2.5.0 rlang_1.1.4 magrittr_2.0.3 ade4_1.7-22 compiler_4.4.1
[7] systemfonts_1.1.0 callr_3.7.6 vctrs_0.6.5 profvis_0.3.8 pkgconfig_2.0.3 crayon_1.5.3
[13] fastmap_1.2.0 ellipsis_0.3.2 fontawesome_0.5.2 utf8_1.2.4 promises_1.3.0 sessioninfo_1.2.2
[19] UCSC.utils_1.1.0 ps_1.7.7 ragg_1.3.2 purrr_1.0.2 xfun_0.46 zlibbioc_1.51.1
[25] cachem_1.1.0 jsonlite_1.8.8 later_1.3.2 R6_2.5.1 bslib_0.8.0 stringi_1.8.4
[31] pkgload_1.4.0 jquerylib_0.1.4 Rcpp_1.0.13 httpuv_1.6.15 tidyselect_1.2.1 rstudioapi_0.16.0
[37] yaml_2.3.10 miniUI_0.1.1.1 curl_5.2.1 processx_3.8.4 pkgbuild_1.4.4 lattice_0.22-6
[43] tibble_3.2.1 plyr_1.8.9 withr_3.0.1 evaluate_0.24.0 desc_1.4.3 urlchecker_1.0.1
[49] zip_2.3.1 pillar_1.9.0 BiocManager_1.30.23 renv_1.0.7 generics_0.1.3 munsell_0.5.1
[55] scales_1.3.0 xtable_1.8-4 glue_1.7.0 lazyeval_0.2.2 fs_1.6.4 grid_4.4.1
[61] tidyr_1.3.1 colorspace_2.1-1 nlme_3.1-165 GenomeInfoDbData_1.2.12 cli_3.6.3 textshaping_0.4.0
[67] fansi_1.0.6 viridisLite_0.4.2 dplyr_1.1.4 gtable_0.3.5 sass_0.4.9 digest_0.6.36
[73] htmlwidgets_1.6.4 memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.12
[79] MASS_7.3-61
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I have tried your solution and it does not seem to work for me. The error message I'm getting is But like @Andreas-Bio and @LinfocitoTh the path is to F: which does not exist in my computer. Please help! Here is my session info
Matrix products: default locale: time zone: America/Chicago attached base packages: other attached packages: loaded via a namespace (and not attached): |
Bug report from Bioconductor Forum: https://support.bioconductor.org/p/134491/
Whenever I try yo launch the Shiny app in R, after having succesfully generated a SangerAlignment file, with the code
launchApp(sangerAlignment)
an error message appears:
"An error has occurred! Couldn't normalize path in 'addResourcePath', with arguments: 'prefix' = 'AdminLTE-2.0.6'; 'directoryPath' = 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/shinydashboard/AdminLTE'
What does it mean? There is no such directory in the computer. The package is installed in another directory. Could this be related? I'm new to Shiny. How could I launch the app?
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