Jordan-Soria
commented
3 years ago Here is all info in detail:
library(BiocManager) Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help BiocManager::valid()
- sessionInfo()
R version 4.0.2 (2020-06-22) Platform: i386-w64-mingw32/i386 (32-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
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] BiocManager_1.30.10
loaded via a namespace (and not attached): [1] compiler_4.0.2 tools_4.0.2 yaml_2.2.1
Bioconductor version '3.12'
- 26 packages out-of-date
- 0 packages too new
create a valid installation with
BiocManager::install(c( "BiocParallel", "bookdown", "broom", "callr", "cli", "cpp11", "data.table", "digest", "DT", "e1071", "foreach", "iterators", "labeling", "MatrixGenerics", "multtest", "phyloseq", "quantreg", "rgdal", "rhdf5", "Rhdf5lib", "rlang", "rmarkdown", "S4Vectors", "seqinr", "statmod", "tibble" ), update = TRUE, ask = FALSE)
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
Warning message: 26 packages out-of-date; 0 packages too new
library(sangeranalyseR) Loading required package: stringr Loading required package: ape Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLBThe following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabsThe following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get,
grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position,
rank, rbind, Reduce, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.minLoading required package: S4Vectors Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.gridLoading required package: IRanges
Attaching package: ‘IRanges’
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windowsLoading required package: XVector
Attaching package: ‘Biostrings’
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complementThe following object is masked from ‘package:base’:
strsplitLoading required package: DECIPHER Loading required package: RSQLite Loading required package: reshape2 Loading required package: phangorn Loading required package: sangerseqR Loading required package: gridExtra
Attaching package: ‘gridExtra’
The following object is masked from ‘package:BiocGenerics’:
combineLoading required package: shiny Loading required package: shinydashboard
Attaching package: ‘shinydashboard’
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boxLoading required package: shinyjs You can use shinyjs to call your own JavaScript functions: https://deanattali.com/shinyjs/extend
Attaching package: ‘shinyjs’
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runExampleThe following object is masked from ‘package:RSQLite’:
showThe following object is masked from ‘package:Biostrings’:
showThe following object is masked from ‘package:XVector’:
showThe following object is masked from ‘package:IRanges’:
showThe following object is masked from ‘package:S4Vectors’:
showThe following object is masked from ‘package:stats4’:
showThe following objects are masked from ‘package:methods’:
removeClass, showLoading required package: data.table data.table 1.13.0 using 2 threads (see ?getDTthreads). Latest news: r-datatable.com
Attaching package: ‘data.table’
The following objects are masked from ‘package:reshape2’:
dcast, meltThe following object is masked from ‘package:IRanges’:
shiftThe following objects are masked from ‘package:S4Vectors’:
first, secondLoading required package: plotly Loading required package: ggplot2
Attaching package: ‘plotly’
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last_plotThe following object is masked from ‘package:XVector’:
sliceThe following object is masked from ‘package:IRanges’:
sliceThe following object is masked from ‘package:S4Vectors’:
renameThe following object is masked from ‘package:stats’:
filterThe following object is masked from ‘package:graphics’:
layoutLoading required package: DT
Attaching package: ‘DT’
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dataTableOutput, renderDataTableLoading required package: zeallot Loading required package: excelR Loading required package: shinycssloaders Loading required package: ggdendro Loading required package: shinyWidgets
Attaching package: ‘shinyWidgets’
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alertLoading required package: openxlsx Loading required package: tools Loading required package: rmarkdown Loading required package: kableExtra Loading required package: seqinr
Attaching package: ‘seqinr’
The following object is masked from ‘package:shiny’:
aThe following object is masked from ‘package:sangerseqR’:
read.abifThe following object is masked from ‘package:Biostrings’:
translateThe following objects are masked from ‘package:ape’:
as.alignment, consensusLoading required package: BiocStyle
Attaching package: ‘BiocStyle’
The following objects are masked from ‘package:rmarkdown’:
html_document, md_document, pdf_documentThe following object is masked from ‘package:shiny’:
markdownLoading required package: logger Welcome to sangeranalyseR
in my example I have four readings (.ab1)
list.files("C:\Users\JORDAN\Desktop\test_R_sanger_join") [1] "Cruces1_c1_M13F.ab1" "Cruces1_c1_M13R.ab1" "Cruces1_c2_M13F.ab1" [4] "Cruces1_c2_M13R.ab1" my_aligned_contigs <- SangerAlignment(parentDirectory = "C:\Users\JORDAN\Desktop\test_R_sangerjoin", suffixForwardRegExp = "[0-9]+F+", suffixReverseRegExp = "[0-9]+_R+") INFO [2020-21-10 11:41:55] * INFO [2020-21-10 11:41:55] Start creating SangerAlignment instance INFO [2020-21-10 11:41:55] * INFO [2020-21-10 11:41:55] **** You are using Regex Method to group AB1 files! SUCCESS [2020-21-10 11:41:55] >> 'SangerAlignment' S4 instance is created !! View(my_aligned_contigs) launchApp(my_aligned_contigs) INFO [2020-21-10 11:42:09] Your input is 'SangerAlignment' S4 instance INFO [2020-21-10 11:42:09] >>> outputDir : C:\Users\JORDAN\AppData\Local\Temp\RtmpS2126X
Listening on http://127.0.0.1:3646
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'
[No stack trace available]
The browser opens with this message: "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"writeFasta("C:\Users\JORDAN\Desktop\test_R_sanger_join") ERROR [2020-21-10 11:42:25] 'object' must be S4 instance! writeFasta(my_aligned_contigs) INFO [2020-21-10 11:42:29] Your input is 'SangerAlignment' S4 instance INFO [2020-21-10 11:42:29] >>> outputDir : C:\Users\JORDAN\AppData\Local\Temp\RtmpS2126X INFO [2020-21-10 11:42:29] Start to write 'SangerAlignment' to FASTA format ... INFO [2020-21-10 11:42:29] >> Writing 'alignment' to FASTA ... Error in writeXStringSet(alignmentObject, file.path(outputDir, "Sanger_contigs_alignment.fa"), : 'x' must be an XStringSet object writeFasta(my_aligned_contigs, outputDir = "C:\Users\JORDAN\Desktop\test_R_sanger_join") INFO [2020-21-10 11:42:32] Your input is 'SangerAlignment' S4 instance INFO [2020-21-10 11:42:32] >>> outputDir : C:\Users\JORDAN\Desktop\test_R_sanger_join INFO [2020-21-10 11:42:32] Start to write 'SangerAlignment' to FASTA format ... INFO [2020-21-10 11:42:32] >> Writing 'alignment' to FASTA ... Error in writeXStringSet(alignmentObject, file.path(outputDir, "Sanger_contigs_alignment.fa"), : 'x' must be an XStringSet object sessionInfo() R version 4.0.2 (2020-06-22) Platform: i386-w64-mingw32/i386 (32-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
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] tools stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] sangeranalyseR_0.99.28 logger_0.1 BiocStyle_2.17.1
[4] seqinr_3.6-1 kableExtra_1.2.1 rmarkdown_2.4
[7] openxlsx_4.2.2 shinyWidgets_0.5.4 ggdendro_0.1.22
[10] shinycssloaders_1.0.0 excelR_0.4.0 zeallot_0.1.0
[13] DT_0.15 plotly_4.9.2.1 ggplot2_3.3.2
[16] data.table_1.13.0 shinyjs_2.0.0 shinydashboard_0.7.1
[19] shiny_1.5.0 gridExtra_2.3 sangerseqR_1.25.0
[22] phangorn_2.5.5 reshape2_1.4.4 DECIPHER_2.17.1
[25] RSQLite_2.2.1 Biostrings_2.57.2 XVector_0.29.3
[28] IRanges_2.23.10 S4Vectors_0.27.13 BiocGenerics_0.35.4
[31] ape_5.4-1 stringr_1.4.0 BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] nlme_3.1-148 bit64_4.0.5 webshot_0.5.2 httr_1.4.2
[5] R6_2.4.1 DBI_1.1.0 lazyeval_0.2.2 colorspace_1.4-1
[9] ade4_1.7-15 withr_2.3.0 tidyselect_1.1.0 bit_4.0.4
[13] compiler_4.0.2 rvest_0.3.6 xml2_1.3.2 scales_1.1.1
[17] quadprog_1.5-8 digest_0.6.25 pkgconfig_2.0.3 htmltools_0.5.0
[21] fastmap_1.0.1 htmlwidgets_1.5.2 rlang_0.4.7 rstudioapi_0.11
[25] generics_0.0.2 jsonlite_1.7.1 dplyr_1.0.2 zip_2.1.1
[29] magrittr_1.5 Matrix_1.2-18 Rcpp_1.0.5 munsell_0.5.0
[33] lifecycle_0.2.0 stringi_1.5.3 yaml_2.2.1 MASS_7.3-51.6
[37] zlibbioc_1.35.0 plyr_1.8.6 grid_4.0.2 blob_1.2.1
[41] promises_1.1.1 crayon_1.3.4 lattice_0.20-41 knitr_1.30
[45] pillar_1.4.6 igraph_1.2.6 fastmatch_1.1-0 glue_1.4.2
[49] evaluate_0.14 vctrs_0.3.4 httpuv_1.5.4 gtable_0.3.0
[53] purrr_0.3.4 tidyr_1.1.2 xfun_0.18 mime_0.9
[57] xtable_1.8-4 later_1.1.0.1 viridisLite_0.3.0 tibble_3.0.3
[61] memoise_1.1.0 ellipsis_0.3.1
Kuanhao-Chao
roblanf
Virginia-b
Risingsun93
sghignone
R problem SangeranalyseR workflow: