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object 'generate_germline_sequence' not found #407

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royfrancis opened this issue Apr 17, 2024 · 0 comments
Open

object 'generate_germline_sequence' not found #407

royfrancis opened this issue Apr 17, 2024 · 0 comments

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@royfrancis
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    library(immunarch)
#> Loading required package: ggplot2
#> Loading required package: dplyr
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> Loading required package: dtplyr
#> Loading required package: data.table
#> 
#> Attaching package: 'data.table'
#> The following objects are masked from 'package:dplyr':
#> 
#>     between, first, last
#> Loading required package: patchwork
    data(immdata)
    align <- immdata$data %>% seqCluster(seqDist(immdata$data), 
        .perc_similarity = 0.6) %>% repGermline(.threads = 8) %>% 
        repAlignLineage(.min_lineage_sequences = 2, .align_threads = 8)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `length_value = map_chr(.y, ~ifelse(all(.x == .x[1]), yes =
#>   .x[1], no = glue("range_{min(.x)}:{max(.x)}")))`.
#> Caused by warning:
#> ! Automatic coercion from integer to character was deprecated in purrr 1.0.0.
#> ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
#> ℹ The deprecated feature was likely used in the immunarch package.
#>   Please report the issue at <https://github.com/immunomind/immunarch/issues>.
#> Error in `map2()`:
#> ℹ In index: 1.
#> ℹ With name: A2-i129.
#> Caused by error in `get()`:
#> ! object 'generate_germline_sequence' not found

Created on 2024-04-17 with reprex v2.1.0

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.2 (2023-10-31)
#>  os       Ubuntu 22.04.3 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Etc/UTC
#>  date     2024-04-17
#>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package       * version date (UTC) lib source
#>  abind           1.4-5   2016-07-21 [1] RSPM (R 4.3.0)
#>  ape             5.7-1   2023-03-13 [1] RSPM (R 4.3.0)
#>  backports       1.4.1   2021-12-13 [1] RSPM (R 4.3.0)
#>  broom           1.0.5   2023-06-09 [1] RSPM (R 4.3.0)
#>  car             3.1-2   2023-03-30 [1] RSPM (R 4.3.0)
#>  carData         3.0-5   2022-01-06 [1] RSPM (R 4.3.0)
#>  cellranger      1.1.0   2016-07-27 [1] RSPM (R 4.3.0)
#>  circlize        0.4.16  2024-02-20 [1] RSPM (R 4.3.0)
#>  class           7.3-22  2023-05-03 [2] CRAN (R 4.3.2)
#>  cli             3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
#>  cluster         2.1.4   2022-08-22 [2] CRAN (R 4.3.2)
#>  codetools       0.2-19  2023-02-01 [2] CRAN (R 4.3.2)
#>  colorspace      2.1-0   2023-01-23 [1] RSPM (R 4.3.0)
#>  data.table    * 1.15.0  2024-01-30 [1] RSPM (R 4.3.0)
#>  DEoptimR        1.1-3   2023-10-07 [1] RSPM (R 4.3.0)
#>  digest          0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
#>  diptest         0.77-0  2023-11-27 [1] RSPM (R 4.3.0)
#>  doParallel      1.0.17  2022-02-07 [1] RSPM (R 4.3.0)
#>  dplyr         * 1.1.4   2023-11-17 [1] RSPM (R 4.3.0)
#>  dtplyr        * 1.3.1   2023-03-22 [1] RSPM (R 4.3.0)
#>  ellipsis        0.3.2   2021-04-29 [1] RSPM (R 4.3.0)
#>  evaluate        0.23    2023-11-01 [1] RSPM (R 4.3.0)
#>  factoextra      1.0.7   2020-04-01 [1] RSPM (R 4.3.0)
#>  fansi           1.0.6   2023-12-08 [1] RSPM (R 4.3.0)
#>  farver          2.1.1   2022-07-06 [1] RSPM (R 4.3.0)
#>  fastmap         1.1.1   2023-02-24 [1] RSPM (R 4.3.0)
#>  fastmatch       1.1-4   2023-08-18 [1] RSPM (R 4.3.0)
#>  flexmix         2.3-19  2023-03-16 [1] RSPM (R 4.3.0)
#>  foreach         1.5.2   2022-02-02 [1] RSPM (R 4.3.0)
#>  fpc             2.2-11  2023-12-15 [1] RSPM (R 4.3.0)
#>  fs              1.6.3   2023-07-20 [1] RSPM (R 4.3.0)
#>  generics        0.1.3   2022-07-05 [1] RSPM (R 4.3.0)
#>  ggalluvial      0.12.5  2023-02-22 [1] RSPM (R 4.3.0)
#>  ggforce         0.4.1   2022-10-04 [1] RSPM (R 4.3.0)
#>  ggplot2       * 3.4.4   2023-10-12 [1] RSPM (R 4.3.0)
#>  ggpubr          0.6.0   2023-02-10 [1] RSPM (R 4.3.0)
#>  ggraph          2.1.0   2022-10-09 [1] RSPM (R 4.3.0)
#>  ggrepel         0.9.5   2024-01-10 [1] RSPM (R 4.3.0)
#>  ggseqlogo       0.2     2024-02-09 [1] RSPM (R 4.3.0)
#>  ggsignif        0.6.4   2022-10-13 [1] RSPM (R 4.3.0)
#>  GlobalOptions   0.1.2   2020-06-10 [1] RSPM (R 4.3.0)
#>  glue            1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
#>  graphlayouts    1.1.0   2024-01-19 [1] RSPM (R 4.3.0)
#>  gridExtra       2.3     2017-09-09 [1] RSPM (R 4.3.0)
#>  gtable          0.3.4   2023-08-21 [1] RSPM (R 4.3.0)
#>  hms             1.1.3   2023-03-21 [1] RSPM (R 4.3.0)
#>  htmltools       0.5.7   2023-11-03 [1] RSPM (R 4.3.0)
#>  httpuv          1.6.14  2024-01-26 [1] RSPM (R 4.3.0)
#>  igraph          2.0.1.1 2024-01-30 [1] RSPM (R 4.3.0)
#>  immunarch     * 0.9.1   2024-03-18 [1] RSPM (R 4.3.0)
#>  iterators       1.0.14  2022-02-05 [1] RSPM (R 4.3.0)
#>  jsonlite        1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
#>  kernlab         0.9-32  2023-01-31 [1] RSPM (R 4.3.0)
#>  knitr           1.45    2023-10-30 [1] RSPM (R 4.3.0)
#>  later           1.3.2   2023-12-06 [1] RSPM (R 4.3.0)
#>  lattice         0.21-9  2023-10-01 [2] CRAN (R 4.3.2)
#>  lifecycle       1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
#>  magrittr        2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
#>  MASS            7.3-60  2023-05-04 [2] CRAN (R 4.3.2)
#>  Matrix          1.6-4   2023-11-30 [1] RSPM (R 4.3.0)
#>  mclust          6.1     2024-02-23 [1] RSPM (R 4.3.0)
#>  mime            0.12    2021-09-28 [1] RSPM (R 4.3.0)
#>  modeltools      0.2-23  2020-03-05 [1] RSPM (R 4.3.0)
#>  munsell         0.5.0   2018-06-12 [1] RSPM (R 4.3.0)
#>  nlme            3.1-163 2023-08-09 [2] CRAN (R 4.3.2)
#>  nnet            7.3-19  2023-05-03 [2] CRAN (R 4.3.2)
#>  patchwork     * 1.2.0   2024-01-08 [1] RSPM (R 4.3.0)
#>  phangorn        2.11.1  2023-01-23 [1] RSPM (R 4.3.0)
#>  pheatmap        1.0.12  2019-01-04 [1] RSPM (R 4.3.0)
#>  pillar          1.9.0   2023-03-22 [1] RSPM (R 4.3.0)
#>  pkgconfig       2.0.3   2019-09-22 [1] RSPM (R 4.3.0)
#>  plyr            1.8.9   2023-10-02 [1] RSPM (R 4.3.0)
#>  polyclip        1.10-6  2023-09-27 [1] RSPM (R 4.3.0)
#>  prabclus        2.3-3   2023-10-24 [1] RSPM (R 4.3.0)
#>  promises        1.2.1   2023-08-10 [1] RSPM (R 4.3.0)
#>  purrr           1.0.2   2023-08-10 [1] RSPM (R 4.3.0)
#>  quadprog        1.5-8   2019-11-20 [1] RSPM (R 4.3.0)
#>  R.cache         0.16.0  2022-07-21 [1] RSPM
#>  R.methodsS3     1.8.2   2022-06-13 [1] RSPM
#>  R.oo            1.26.0  2024-01-24 [1] RSPM (R 4.3.0)
#>  R.utils         2.12.3  2023-11-18 [1] RSPM
#>  R6              2.5.1   2021-08-19 [1] RSPM (R 4.3.0)
#>  RColorBrewer    1.1-3   2022-04-03 [1] RSPM (R 4.3.0)
#>  Rcpp            1.0.12  2024-01-09 [1] RSPM (R 4.3.0)
#>  readr           2.1.5   2024-01-10 [1] RSPM (R 4.3.0)
#>  readxl          1.4.3   2023-07-06 [1] RSPM (R 4.3.0)
#>  reprex          2.1.0   2024-01-11 [1] RSPM (R 4.3.0)
#>  reshape2        1.4.4   2020-04-09 [1] RSPM (R 4.3.0)
#>  rlang           1.1.3   2024-01-10 [1] RSPM (R 4.3.0)
#>  rlist           0.4.6.2 2021-09-03 [1] RSPM (R 4.3.0)
#>  rmarkdown       2.25    2023-09-18 [1] RSPM
#>  robustbase      0.99-2  2024-01-27 [1] RSPM (R 4.3.0)
#>  rstatix         0.7.2   2023-02-01 [1] RSPM (R 4.3.0)
#>  scales          1.3.0   2023-11-28 [1] RSPM (R 4.3.0)
#>  sessioninfo     1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
#>  shape           1.4.6   2021-05-19 [1] RSPM (R 4.3.0)
#>  shiny           1.8.0   2023-11-17 [1] RSPM (R 4.3.0)
#>  shinythemes     1.2.0   2021-01-25 [1] RSPM (R 4.3.0)
#>  stringdist      0.9.12  2023-11-28 [1] RSPM (R 4.3.0)
#>  stringi         1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
#>  stringr         1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
#>  styler          1.10.2  2023-08-29 [1] RSPM
#>  tibble          3.2.1   2023-03-20 [1] RSPM (R 4.3.0)
#>  tidygraph       1.3.1   2024-01-30 [1] RSPM (R 4.3.0)
#>  tidyr           1.3.1   2024-01-24 [1] RSPM (R 4.3.0)
#>  tidyselect      1.2.0   2022-10-10 [1] RSPM (R 4.3.0)
#>  tweenr          2.0.2   2022-09-06 [1] RSPM (R 4.3.0)
#>  tzdb            0.4.0   2023-05-12 [1] RSPM (R 4.3.0)
#>  UpSetR          1.4.0   2019-05-22 [1] RSPM (R 4.3.0)
#>  utf8            1.2.4   2023-10-22 [1] RSPM (R 4.3.0)
#>  uuid            1.2-0   2024-01-14 [1] RSPM (R 4.3.0)
#>  vctrs           0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
#>  viridis         0.6.5   2024-01-29 [1] RSPM (R 4.3.0)
#>  viridisLite     0.4.2   2023-05-02 [1] RSPM (R 4.3.0)
#>  withr           3.0.0   2024-01-16 [1] RSPM (R 4.3.0)
#>  xfun            0.41    2023-11-01 [1] RSPM (R 4.3.0)
#>  xtable          1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
#>  yaml            2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
#> 
#>  [1] /usr/local/lib/R/site-library
#>  [2] /usr/local/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
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@royfrancis