Open Kuanhao-Chao opened 3 years ago
Kuanhao-Chao
commented
3 years ago shinydashboard package is used to create dashboards of Shiny applications embedded in sangeranalyseR. It seems like a version conflict issue to me now. Could you please provide your R session information sessionInfo() and a simple reproducible example here so that I can do some testing? Thanks a lot!
bomsterr
commented
3 years ago I also get this error, I typed sessionInfo() and got the following:
dracoplasma
commented
3 years ago Hi, I'm the original poster. I created the path specified in "'C:/Users/biocbuild/bbs-3.12-bioc/R/library/shinydashboard/AdminLTE" (empty folders) and the app launches. But the graphs and results don't appear. I'm away from my computer now, but I will provide sessionInfo and screenshots.
Kuanhao-Chao
commented
3 years ago Hi @dracoplasma, @bomsterr
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
Kuanhao-Chao
commented
3 years ago Hi @dracoplasma, @bomsterr
I have updated the R package in the latest commit. Please check whether the graphs and results appear in Shiny apps (launchApp function) and also RMarkdown reports (generateReport function).
@bomsterr Could you run with your data again to see whether you can launch the app now? Thanks a lot.
cheers,
Howard
bomsterr
commented
3 years ago Hi Howard,
I ran launchApp(sangerAlignment) and got the same error again:
Warning: Error in value[[3L]]: 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'
AlexGaithuma
commented
3 years ago Hi Howard,
I also got the same error.
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
system code page: 65001
attached base packages:
[1] tools stats4 parallel stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] sangeranalyseR_1.0.0 logger_0.1 BiocStyle_2.18.1 seqinr_4.2-5
[5] kableExtra_1.3.1 rmarkdown_2.6 openxlsx_4.2.3 shinyWidgets_0.5.5
[9] ggdendro_0.1.22 shinycssloaders_1.0.0 excelR_0.4.0 zeallot_0.1.0
[13] DT_0.17 plotly_4.9.3 ggplot2_3.3.3 data.table_1.13.6
[17] shinyjs_2.0.0 shinydashboard_0.7.1 shiny_1.5.0 gridExtra_2.3
[21] sangerseqR_1.26.0 phangorn_2.5.5 reshape2_1.4.4 DECIPHER_2.18.1
[25] RSQLite_2.2.2 Biostrings_2.58.0 XVector_0.30.0 IRanges_2.24.1
[29] S4Vectors_0.28.1 BiocGenerics_0.36.0 ape_5.4-1 stringr_1.4.0
loaded via a namespace (and not attached):
[1] nlme_3.1-151 bit64_4.0.5 webshot_0.5.2 progress_1.2.2
[5] httr_1.4.2 R6_2.5.0 DBI_1.1.1 lazyeval_0.2.2
[9] colorspace_2.0-0 ade4_1.7-16 withr_2.4.0 tidyselect_1.1.0
[13] prettyunits_1.1.1 bit_4.0.4 compiler_4.0.3 rvest_0.3.6
[17] xml2_1.3.2 scales_1.1.1 quadprog_1.5-8 digest_0.6.27
[21] pkgconfig_2.0.3 htmltools_0.5.0 fastmap_1.0.1 htmlwidgets_1.5.3
[25] rlang_0.4.10 rstudioapi_0.13 generics_0.1.0 jsonlite_1.7.2
[29] dplyr_1.0.2 zip_2.1.1 magrittr_2.0.1 Matrix_1.2-18
[33] Rcpp_1.0.5 munsell_0.5.0 lifecycle_0.2.0 yaml_2.2.1
[37] stringi_1.5.3 MASS_7.3-53 zlibbioc_1.36.0 plyr_1.8.6
[41] grid_4.0.3 blob_1.2.1 promises_1.1.1 crayon_1.3.4
[45] lattice_0.20-41 hms_1.0.0 knitr_1.30 pillar_1.4.7
[49] igraph_1.2.6 fastmatch_1.1-0 glue_1.4.2 evaluate_0.14
[53] BiocManager_1.30.10 vctrs_0.3.6 httpuv_1.5.4 gtable_0.3.0
[57] purrr_0.3.4 tidyr_1.1.2 xfun_0.20 mime_0.9
[61] xtable_1.8-4 later_1.1.0.1 viridisLite_0.3.0 tibble_3.0.4
[65] memoise_1.1.0 ellipsis_0.3.1 
SilonovSA
commented
3 years ago Hi, Howard,
I tried to run SangerAnalyzer according to https://sangeranalyser.readthedocs.io/en/latest/content/beginner.html, but had the same mistake: [ 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' ].
Are there any variants to solve this problem?
I hope for your help >.<
sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale: [1] LC_COLLATE=Russian_Russia.1251 LC_CTYPE=Russian_Russia.1251 LC_MONETARY=Russian_Russia.1251 [4] LC_NUMERIC=C LC_TIME=Russian_Russia.1251
attached base packages: [1] tools stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] sangeranalyseR_1.0.0 logger_0.2.0 BiocStyle_2.18.1 seqinr_4.2-5 kableExtra_1.3.4
[6] rmarkdown_2.7 openxlsx_4.2.3 shinyWidgets_0.5.7 ggdendro_0.1.22 shinycssloaders_1.0.0
[11] excelR_0.4.0 zeallot_0.1.0 DT_0.17 plotly_4.9.3 ggplot2_3.3.3
[16] data.table_1.14.0 shinyjs_2.0.0 shinydashboard_0.7.1 shiny_1.6.0 gridExtra_2.3
[21] sangerseqR_1.26.0 phangorn_2.5.5 reshape2_1.4.4 DECIPHER_2.18.1 RSQLite_2.2.3
[26] Biostrings_2.58.0 XVector_0.30.0 IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0
[31] ape_5.4-1 stringr_1.4.0
loaded via a namespace (and not attached):
[1] nlme_3.1-152 bit64_4.0.5 progress_1.2.2 webshot_0.5.2 httr_1.4.2 bslib_0.2.4
[7] utf8_1.1.4 R6_2.5.0 DBI_1.1.1 lazyeval_0.2.2 colorspace_2.0-0 ade4_1.7-16
[13] withr_2.4.1 prettyunits_1.1.1 tidyselect_1.1.0 bit_4.0.4 compiler_4.0.4 rvest_0.3.6
[19] xml2_1.3.2 sass_0.3.1 scales_1.1.1 quadprog_1.5-8 systemfonts_1.0.1 digest_0.6.27
[25] svglite_2.0.0 pkgconfig_2.0.3 htmltools_0.5.1.1 fastmap_1.1.0 htmlwidgets_1.5.3 rlang_0.4.10
[31] rstudioapi_0.13 jquerylib_0.1.3 generics_0.1.0 jsonlite_1.7.2 dplyr_1.0.5 zip_2.1.1
[37] magrittr_2.0.1 Matrix_1.3-2 Rcpp_1.0.6 munsell_0.5.0 fansi_0.4.2 lifecycle_1.0.0
[43] yaml_2.2.1 stringi_1.5.3 MASS_7.3-53 zlibbioc_1.36.0 plyr_1.8.6 grid_4.0.4
[49] blob_1.2.1 promises_1.2.0.1 crayon_1.4.1 lattice_0.20-41 hms_1.0.0 knitr_1.31
[55] pillar_1.5.1 igraph_1.2.6 fastmatch_1.1-0 glue_1.4.2 evaluate_0.14 BiocManager_1.30.10
[61] vctrs_0.3.6 httpuv_1.5.5 gtable_0.3.0 purrr_0.3.4 tidyr_1.1.3 cachem_1.0.4
[67] xfun_0.21 mime_0.10 xtable_1.8-4 later_1.1.0.1 viridisLite_0.3.0 tibble_3.1.0
[73] memoise_2.0.0 ellipsis_0.3.1
Virginia-b
commented
3 years ago Hi Howard,
I have also the same problem when I try to launch Shiny app using
launchApp(my_aligned_contigs)
sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 [4] LC_NUMERIC=C LC_TIME=Spanish_Spain.1252
attached base packages: [1] tools stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] sangeranalyseR_1.0.0 logger_0.2.0 BiocStyle_2.18.1 seqinr_4.2-5 kableExtra_1.3.4
[6] rmarkdown_2.7 openxlsx_4.2.3 shinyWidgets_0.6.0 ggdendro_0.1.22 shinycssloaders_1.0.0
[11] excelR_0.4.0 zeallot_0.1.0 DT_0.17 plotly_4.9.3 ggplot2_3.3.3
[16] data.table_1.14.0 shinyjs_2.0.0 shinydashboard_0.7.1 shiny_1.6.0 gridExtra_2.3
[21] sangerseqR_1.26.0 phangorn_2.5.5 reshape2_1.4.4 DECIPHER_2.18.1 RSQLite_2.2.4
[26] Biostrings_2.58.0 XVector_0.30.0 IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0
[31] ape_5.4-1 stringr_1.4.0
loaded via a namespace (and not attached):
[1] nlme_3.1-152 bit64_4.0.5 progress_1.2.2 webshot_0.5.2 httr_1.4.2
[6] bslib_0.2.4 utf8_1.2.1 R6_2.5.0 DBI_1.1.1 lazyeval_0.2.2
[11] colorspace_2.0-0 ade4_1.7-16 withr_2.4.1 prettyunits_1.1.1 tidyselect_1.1.0
[16] bit_4.0.4 compiler_4.0.4 rvest_1.0.0 xml2_1.3.2 sass_0.3.1
[21] scales_1.1.1 quadprog_1.5-8 systemfonts_1.0.1 digest_0.6.27 svglite_2.0.0
[26] pkgconfig_2.0.3 htmltools_0.5.1.1 fastmap_1.1.0 htmlwidgets_1.5.3 rlang_0.4.10
[31] rstudioapi_0.13 jquerylib_0.1.3 generics_0.1.0 jsonlite_1.7.2 dplyr_1.0.5
[36] zip_2.1.1 magrittr_2.0.1 Matrix_1.3-2 Rcpp_1.0.6 munsell_0.5.0
[41] fansi_0.4.2 lifecycle_1.0.0 yaml_2.2.1 stringi_1.5.3 MASS_7.3-53.1
[46] zlibbioc_1.36.0 plyr_1.8.6 grid_4.0.4 blob_1.2.1 promises_1.2.0.1
[51] crayon_1.4.1 lattice_0.20-41 hms_1.0.0 knitr_1.31 pillar_1.5.1
[56] igraph_1.2.6 fastmatch_1.1-0 glue_1.4.2 evaluate_0.14 BiocManager_1.30.10
[61] vctrs_0.3.6 httpuv_1.5.5 gtable_0.3.0 purrr_0.3.4 tidyr_1.1.3
[66] cachem_1.0.4 xfun_0.22 mime_0.10 xtable_1.8-4 later_1.1.0.1
[71] viridisLite_0.3.0 tibble_3.1.0 memoise_2.0.0 ellipsis_0.3.1
Thank you.
Cheers, Virginia
Kuanhao-Chao
commented
3 years ago Hi @bomsterr, @AlexGaithuma, @SilonovSA, @Virginia-b,
Sorry for the late reply. This is a bizarre bug for me. I tried sangeranalyseR on the macOS 10.15 and Windows 10, and did some experiments; however, I just couldn't duplicate the same error. I guess in some conditions, the shinydashboard package that sangeranalyseR depends on could not handle this AdminLTE path error. Could you install sangeranalyseR from the latest commit in development branch and try @dracoplasma 's solution to see whether it works?
Hi, I'm the original poster. I created the path specified in "'C:/Users/biocbuild/bbs-3.12-bioc/R/library/shinydashboard/AdminLTE" (empty folders) and the app launches. But the graphs and results don't appear. I'm away from my computer now, but I will provide sessionInfo and screenshots.
Here is the way to install sangeranalyseR with the latest version.
library(devtools)
install_github("roblanf/sangeranalyseR", ref = "develop")
library(sangeranalyseR)Thanks!
Howard
Andreas-Bio
commented
2 years ago Listening on http://127.0.0.1:5501
Warning: Error in value[[3L]]: Couldn't normalize path in `addResourcePath`, with arguments: `prefix` = 'AdminLTE-2.0.6'; `directoryPath` = 'F:/biocbuild/bbs-3.15-bioc/R/library/shinydashboard/AdminLTE'
[No stack trace available]
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.utf8 LC_CTYPE=English_Canada.utf8 LC_MONETARY=English_Canada.utf8
[4] LC_NUMERIC=C LC_TIME=English_Canada.utf8
attached base packages:
[1] tools parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] sangeranalyseR_1.6.1 logger_0.2.2 BiocStyle_2.24.0 seqinr_4.2-16 knitr_1.39
[6] rmarkdown_2.14 openxlsx_4.2.5 shinyWidgets_0.7.0 ggdendro_0.1.23 shinycssloaders_1.0.0
[11] excelR_0.4.0 zeallot_0.1.0 DT_0.23 plotly_4.10.0 ggplot2_3.3.6
[16] data.table_1.14.2 shinyjs_2.1.0 shinydashboard_0.7.2 shiny_1.7.1 gridExtra_2.3
[21] phangorn_2.9.0 reshape2_1.4.4 DECIPHER_2.24.0 RSQLite_2.2.14 ape_5.6-2
[26] stringr_1.4.0 sangerseqR_1.32.0 Biostrings_2.64.0 GenomeInfoDb_1.32.2 XVector_0.36.0
[31] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 BiocManager_1.30.18
loaded via a namespace (and not attached):
[1] nlme_3.1-157 bitops_1.0-7 bit64_4.0.5 httr_1.4.3 bslib_0.3.1
[6] utf8_1.2.2 R6_2.5.1 DBI_1.1.3 lazyeval_0.2.2 colorspace_2.0-3
[11] ade4_1.7-19 withr_2.5.0 tidyselect_1.1.2 bit_4.0.4 compiler_4.2.1
[16] cli_3.3.0 sass_0.4.1 scales_1.2.0 quadprog_1.5-8 digest_0.6.29
[21] pkgconfig_2.0.3 htmltools_0.5.2 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.2
[26] jquerylib_0.1.4 generics_0.1.2 jsonlite_1.8.0 dplyr_1.0.9 zip_2.2.0
[31] RCurl_1.98-1.7 magrittr_2.0.3 GenomeInfoDbData_1.2.8 Matrix_1.4-1 Rcpp_1.0.8.3
[36] munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.1 yaml_2.3.5 stringi_1.7.6
[41] MASS_7.3-57 zlibbioc_1.42.0 plyr_1.8.7 grid_4.2.1 blob_1.2.3
[46] promises_1.2.0.1 crayon_1.5.1 lattice_0.20-45 pillar_1.7.0 igraph_1.3.2
[51] codetools_0.2-18 fastmatch_1.1-3 glue_1.6.2 evaluate_0.15 vctrs_0.4.1
[56] httpuv_1.6.5 gtable_0.3.0 purrr_0.3.4 tidyr_1.2.0 cachem_1.0.6
[61] xfun_0.31 mime_0.12 xtable_1.8-4 later_1.3.0 viridisLite_0.4.0
[66] tibble_3.1.7 memoise_2.0.1 ellipsis_0.3.2
I have a similar issue. I don't even know what F is. That letter is not assigned to any harddrive or network resource on my machine. So I can't even create an empty folder because I have no "F" drive.
LinfocitoTh
commented
1 year ago 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!
Couldn't normalize path in addResourcePath, with arguments: prefix = 'AdminLTE-2.0.6'; directoryPath = 'F:/biocbuild/bbs-3.17-bioc/R/library/shinydashboard/AdminLTE'.
And this corresponds to my data.
sessionInfo() R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)
Stay tuned, thanks <3
Risingsun93
commented
1 year ago @Kuanhao-Chao I'm facing the same problem
valpalgal
commented
7 months ago I also have this same problem on Mac.
JaredSipesBioE
commented
1 month ago 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.
The following document is following the introduction manual given here:
https://sangeranalyser.readthedocs.io/en/latest/index.html
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("sangeranalyseR")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)
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 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, REGEXSuffixForward = "[0-9]_F.ab1$", REGEXSuffixReverse = "[0-9]_R.ab1$")
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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klange2
commented
4 weeks ago @JaredSipesBioE
I have tried your solution and it does not seem to work for me. The error message I'm getting is
Couldn't normalize path in addResourcePath, with arguments: prefix = 'AdminLTE-2.0.6'; directoryPath = 'F:/biocbuild/bbs-3.20-bioc/R/library/shinydashboard/AdminLTE'
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
sessionInfo() R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] 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
[9] methods base
other attached packages:
[1] DBI_1.2.3 textshaping_0.4.0 fontawesome_0.5.2
[4] systemfonts_1.1.0 sangeranalyseR_1.15.0 logger_0.3.0
[7] BiocStyle_2.33.1 seqinr_4.2-36 knitr_1.48
[10] rmarkdown_2.28 openxlsx_4.2.7 shinyWidgets_0.8.6
[13] ggdendro_0.2.0 shinycssloaders_1.1.0 excelR_0.4.0
[16] zeallot_0.1.0 DT_0.33 plotly_4.10.4
[19] ggplot2_3.5.1 data.table_1.16.0 shinyjs_2.1.0
[22] shinydashboard_0.7.2 shiny_1.9.1 gridExtra_2.3
[25] sangerseqR_1.41.0 reshape2_1.4.4 DECIPHER_3.1.4
[28] pwalign_1.1.0 Biostrings_2.73.1 GenomeInfoDb_1.41.1
[31] XVector_0.45.0 IRanges_2.39.2 S4Vectors_0.43.2
[34] BiocGenerics_0.51.0 ape_5.8 stringr_1.5.1
[37] devtools_2.4.5 usethis_3.0.0
loaded via a namespace (and not attached):
[1] remotes_2.5.0 rlang_1.1.4 magrittr_2.0.3
[4] ade4_1.7-22 compiler_4.4.1 callr_3.7.6
[7] vctrs_0.6.5 profvis_0.3.8 pkgconfig_2.0.3
[10] crayon_1.5.3 fastmap_1.2.0 ellipsis_0.3.2
[13] utf8_1.2.4 promises_1.3.0 sessioninfo_1.2.2
[16] UCSC.utils_1.1.0 ps_1.7.7 tinytex_0.52
[19] purrr_1.0.2 xfun_0.47 zlibbioc_1.51.1
[22] cachem_1.1.0 jsonlite_1.8.8 later_1.3.2
[25] R6_2.5.1 bslib_0.8.0 stringi_1.8.4
[28] pkgload_1.4.0 jquerylib_0.1.4 Rcpp_1.0.13
[31] httpuv_1.6.15 tidyselect_1.2.1 rstudioapi_0.16.0
[34] yaml_2.3.10 miniUI_0.1.1.1 curl_5.2.2
[37] processx_3.8.4 pkgbuild_1.4.4 lattice_0.22-6
[40] tibble_3.2.1 plyr_1.8.9 withr_3.0.1
[43] evaluate_0.24.0 desc_1.4.3 urlchecker_1.0.1
[46] zip_2.3.1 pillar_1.9.0 BiocManager_1.30.25
[49] renv_1.0.7 generics_0.1.3 munsell_0.5.1
[52] scales_1.3.0 xtable_1.8-4 glue_1.7.0
[55] lazyeval_0.2.2 fs_1.6.4 grid_4.4.1
[58] tidyr_1.3.1 colorspace_2.1-1 nlme_3.1-166
[61] GenomeInfoDbData_1.2.12 cli_3.6.3 fansi_1.0.6
[64] viridisLite_0.4.2 dplyr_1.1.4 gtable_0.3.5
[67] sass_0.4.9 digest_0.6.37 htmlwidgets_1.6.4
[70] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
[73] httr_1.4.7 mime_0.12 MASS_7.3-61
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?