Kuanhao-Chao
commented
2 years ago Hi @marthaluka,
The version of the sangeranalyseR in your sessionInfo is 1.1.2. I would suggest you to update sangeranalyseR to the newest version, and it should work correctly. We've resolved this issue in the latest update. Thanks!
Best wishes, Kuan-Hao
Hi, I encounter a problem when generating the report using generateReport
`library(sangeranalyseR)
my_aligned_contigs <- SangerAlignment(ABIF_Directory = "./SangerData/", REGEX_SuffixForward = "_F.ab1$", REGEX_SuffixReverse = "_R.ab1$")
launchApp(my_aligned_contigs)
writeFasta(my_aligned_contigs, outputDir = "output/", compress = FALSE, compression_level = NA)
generateReport(my_aligned_contigs, outputDir = "./output/") `
The first three functions work well but generateReport exits with:
File ./Chromatogram.pdf not found in resource path Error: pandoc document conversion failed with error 99This only creates a chromatogram for the first sample (please see attached figure). I think the problem is related to rmarkdown but I'm not sure how to address it.sessionInfo() ` R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] tools stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] sangeranalyseR_1.1.2 logger_0.2.2 BiocStyle_2.18.1 seqinr_4.2-8
[5] kableExtra_1.3.4 rmarkdown_2.13 openxlsx_4.2.5 shinyWidgets_0.6.4
[9] ggdendro_0.1.23 shinycssloaders_1.0.0 excelR_0.4.0 zeallot_0.1.0
[13] DT_0.21 plotly_4.10.0 ggplot2_3.3.5 data.table_1.14.2
[17] shinyjs_2.1.0 shinydashboard_0.7.2 shiny_1.7.1 gridExtra_2.3
[21] sangerseqR_1.26.0 phangorn_2.7.0 reshape2_1.4.4 DECIPHER_2.18.1
[25] RSQLite_2.2.10 Biostrings_2.58.0 XVector_0.30.0 IRanges_2.24.1
[29] S4Vectors_0.28.1 BiocGenerics_0.36.1 ape_5.6-2 stringr_1.4.0
loaded via a namespace (and not attached): [1] nlme_3.1-152 fontawesome_0.2.2 bit64_4.0.5 webshot_0.5.2 httr_1.4.2
[6] rprojroot_2.0.2 bslib_0.3.1 utf8_1.2.2 R6_2.5.1 DBI_1.1.2
[11] lazyeval_0.2.2 colorspace_2.0-3 ade4_1.7-18 withr_2.5.0 tidyselect_1.1.2
[16] bit_4.0.4 compiler_4.0.5 rvest_1.0.2 cli_3.2.0 pacman_0.5.1
[21] xml2_1.3.3 sass_0.4.0 scales_1.1.1 quadprog_1.5-8 systemfonts_1.0.4
[26] digest_0.6.29 svglite_2.1.0 pkgconfig_2.0.3 htmltools_0.5.2 fastmap_1.1.0
[31] htmlwidgets_1.5.4 rlang_1.0.2 rstudioapi_0.13 jquerylib_0.1.4 generics_0.1.2
[36] zoo_1.8-9 jsonlite_1.8.0 crosstalk_1.2.0 dplyr_1.0.8 zip_2.2.0
[41] magrittr_2.0.2 Matrix_1.3-3 Rcpp_1.0.8.2 munsell_0.5.0 fansi_1.0.2
[46] lifecycle_1.0.1 yaml_2.3.5 stringi_1.7.6 MASS_7.3-54 zlibbioc_1.36.0
[51] plyr_1.8.6 grid_4.0.5 blob_1.2.2 promises_1.2.0.1 crayon_1.5.0
[56] lattice_0.20-44 knitr_1.37 pillar_1.7.0 igraph_1.2.6 codetools_0.2-18
[61] fastmatch_1.1-0 glue_1.6.2 evaluate_0.15 BiocManager_1.30.16 vctrs_0.3.8
[66] httpuv_1.6.5 gtable_0.3.0 purrr_0.3.4 tidyr_1.2.0 assertthat_0.2.1
[71] cachem_1.0.6 xfun_0.30 mime_0.12 xtable_1.8-4 later_1.3.0
[76] viridisLite_0.4.0 tibble_3.1.6 tinytex_0.37 memoise_2.0.1 ellipsis_0.3.2
[81] here_1.0.1 `
Kindly assist. Thanks