roblanf
ISSUE SangeranalyseR Shiny app/ launchApp command does not work
Hello everyone,
I am quite new to R and Github as well. Currently, I am working with SangeranalyseR and created several contigs. But the launchApp comand as well as the writeFasta command does not work. Please find attached my code + error messages from the console. Here my code:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("sangeranalyseR") #Step 2: Load and analyse your data------------------ my_aligned_contigs <- SangerAlignment(parentDirectory = "~/MasterUniOldenburg/Masterthesis/Bioinformatics/RP/RP2021_BeneficialBacteria/RCode_ICBM/SangerProcessing", suffixForwardRegExp = "_[0-9]F.ab1$", suffixReverseRegExp = "[0-9]_R.ab1$")
######################
#Step 3: Exploring your data with the shiny app RCode_terminal.txt
launchAppSA(my_aligned_contigs)
#Step4: Write the FASTA files writeFastaSA(my_aligned_contigs)
#step 5: generate report generateReportSA(my_aligned_contigs)
maybe I missed some relevant info? Thanks for help!
Here my session info:
sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] tools stats4 parallel stats graphics grDevices utils datasets [9] methods base
other attached packages:
[1] devtools_2.4.2 usethis_2.0.1 sangeranalyseR_1.0.0
[4] logger_0.2.1 BiocStyle_2.18.1 seqinr_4.2-8
[7] kableExtra_1.3.4 rmarkdown_2.11 openxlsx_4.2.4
[10] shinyWidgets_0.6.2 ggdendro_0.1.22 shinycssloaders_1.0.0
[13] excelR_0.4.0 zeallot_0.1.0 DT_0.19
[16] plotly_4.9.4.1 ggplot2_3.3.5 data.table_1.14.2
[19] shinyjs_2.0.0 shinydashboard_0.7.2 shiny_1.7.1
[22] gridExtra_2.3 sangerseqR_1.26.0 phangorn_2.7.1
[25] reshape2_1.4.4 DECIPHER_2.18.1 RSQLite_2.2.8
[28] Biostrings_2.58.0 XVector_0.30.0 IRanges_2.24.1
[31] S4Vectors_0.28.1 BiocGenerics_0.36.1 ape_5.5
[34] stringr_1.4.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-2 ellipsis_0.3.2 rprojroot_2.0.2 fs_1.5.0
[5] rstudioapi_0.13 remotes_2.4.1 bit64_4.0.5 fansi_0.5.0
[9] xml2_1.3.2 codetools_0.2-18 cachem_1.0.6 knitr_1.36
[13] pkgload_1.2.2 ade4_1.7-18 jsonlite_1.7.2 BiocManager_1.30.16
[17] compiler_4.0.5 httr_1.4.2 assertthat_0.2.1 Matrix_1.3-4
[21] fastmap_1.1.0 lazyeval_0.2.2 cli_3.0.1 later_1.3.0
[25] prettyunits_1.1.1 htmltools_0.5.2 igraph_1.2.6 gtable_0.3.0
[29] glue_1.4.2 dplyr_1.0.7 tinytex_0.34 fastmatch_1.1-3
[33] Rcpp_1.0.7 jquerylib_0.1.4 vctrs_0.3.8 svglite_2.0.0
[37] nlme_3.1-153 crosstalk_1.1.1 xfun_0.26 ps_1.6.0
[41] testthat_3.1.0 rvest_1.0.1 mime_0.12 lifecycle_1.0.1
[45] zlibbioc_1.36.0 MASS_7.3-54 scales_1.1.1 promises_1.2.0.1
[49] curl_4.3.2 yaml_2.2.1 memoise_2.0.0 sass_0.4.0
[53] stringi_1.7.4 desc_1.4.0 pkgbuild_1.2.0 zip_2.2.0
[57] rlang_0.4.11 pkgconfig_2.0.3 systemfonts_1.0.2 evaluate_0.14
[61] lattice_0.20-45 purrr_0.3.4 htmlwidgets_1.5.4 processx_3.5.2
[65] bit_4.0.4 tidyselect_1.1.1 bookdown_0.24 plyr_1.8.6
[69] magrittr_2.0.1 R6_2.5.1 generics_0.1.0 DBI_1.1.1
[73] pillar_1.6.3 withr_2.4.2 tibble_3.1.4 crayon_1.4.1
[77] utf8_1.2.2 grid_4.0.5 blob_1.2.2 callr_3.7.0
[81] digest_0.6.27 webshot_0.5.2 xtable_1.8-4 tidyr_1.1.3
[85] httpuv_1.6.3 munsell_0.5.0 viridisLite_0.4.0 bslib_0.3.1
[89] sessioninfo_1.1.1 quadprog_1.5-8
Hi @MarieRut ,
The examples on the vignettes html are outdated. We have new examples on the sangeranalyeR documentation page, please check here. There are a few examples that you can just copy-paste in the R shell. It should work!
Best, Howard
