StartracDiversity issue #290

mainyanghr · 2023-12-18T02:19:40Z

StartracDiversity(immuneTCRgene, type = "Cancer", sample = "patientNumber", by = "overall")

[2023-12-17 21:13:42.644434] initialize Startrac ...
Error in (function (cl, name, valueClass) :
assignment of an object of class "factor" is not valid for @'clone2patient' in an object of class "Startrac"; is(value, "array") is not TRUE

My data format is combined one. Any comments on that? Thank you very much!

Harry

ncborcherding · 2023-12-18T10:55:06Z

Hey Harry,

Can you give me the output of you sessionInfo()? I still need to know the version you are using.

Nick

mainyanghr · 2023-12-18T15:21:47Z

Thank you very much for your kind help. Please see the information. Thanks

sessionInfo()

Error in `palette()`:
! Must request at least one colour from a hue palette.
Backtrace:
  1. base (local) `<fn>`(x)
  2. patchwork:::print.patchwork(x)
  3. patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
  4. base::lapply(x$plots, plot_table, guides = guides)
  6. patchwork:::plot_table.ggplot(X[[i]], ...)
     ...
 21. ggplot2 (local) FUN(X[[i]], ...)
 22. self$map(df[[j]])
 23. ggplot2 (local) map(..., self = self)
 24. self$palette(n)
 25. scales (local) palette(...)

R Console

Error in `palette()`:
! Must request at least one colour from a hue palette.
Backtrace:
  1. base (local) `<fn>`(x)
  2. patchwork:::print.patchwork(x)
  3. patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
  4. base::lapply(x$plots, plot_table, guides = guides)
  6. patchwork:::plot_table.ggplot(X[[i]], ...)
     ...
 21. ggplot2 (local) FUN(X[[i]], ...)
 22. self$map(df[[j]])
 23. ggplot2 (local) map(..., self = self)
 24. self$palette(n)
 25. scales (local) palette(...)

Show Traceback

Error in palette(...) :

Description:df [10 × 42]

--

[2023-12-17 19:38:59.067222] initialize Startrac ...

Show Traceback

Error in (function (cl, name, valueClass) : assignment of an object of class "factor" is not valid for @'clone2patient' in an object of class "Startrac"; is(value, "array") is not TRUE

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2
Matrix products: default

BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York

tzcode source: internal
attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
 [1] quantreg_5.97 [4] RColorBrewer_1.1-3 [7] Platypus_3.5.0 [10] seqinr_4.2-36 [13] MultiAssayExperiment_1.28.0 [16] Biobase_2.62.0 [19] IRanges_2.36.0 [22] MatrixGenerics_1.14.0 [25] glmGamPoi_1.14.0 [28] BiocManager_1.30.22 [31] Rcpp_1.0.11 [34] viridisLite_0.4.2 [37] sctransform_0.4.1 [40] BPCells_0.1.0 [43] bmcite.SeuratData_0.3.0 [46] patchwork_1.1.3 [49] scales_1.3.0 [52] forcats_1.0.0 [55] purrr_1.0.2 [58] tibble_3.2.1 [61] Seurat_5.0.1 [64] devtools_2.4.5

SparseM_1.81                ggraph_2.1.0
 here_1.0.1                  scRepertoire_1.12.0
 ggtree_3.10.0               useful_1.2.6.1
 celldex_1.12.0              SingleCellMultiModal_1.14.0
 SingleR_2.4.0               SummarizedExperiment_1.32.0
 GenomicRanges_1.54.1        GenomeInfoDb_1.38.1
 S4Vectors_0.40.2            BiocGenerics_0.48.1
 matrixStats_1.2.0           SeuratWrappers_0.3.2
 presto_1.0.0                data.table_1.14.10
 remotes_2.4.2.1             harmony_1.2.0
 ggsci_3.0.0                 viridis_0.6.4
 magrittr_2.0.3              circlize_0.4.15
 Azimuth_0.5.0               shinyBS_0.61.1
 pbmcsca.SeuratData_3.0.0    pbmcref.SeuratData_1.0.0
 SeuratData_0.2.2.9001       SeuratDisk_0.0.0.9021
 RCurl_1.98-1.13             cowplot_1.1.2
 Matrix_1.6-4                lubridate_1.9.3
 stringr_1.5.1               dplyr_1.1.4
 readr_2.1.4                 tidyr_1.3.0
 ggplot2_3.4.4               tidyverse_2.0.0
 SeuratObject_5.0.1          sp_2.1-2
 usethis_2.2.2
loaded via a namespace (and not attached):

[1] igraph_1.6.0                      ica_1.0-3                         plotly_4.10.3

[4] zlibbioc_1.48.0                   tidyselect_1.2.0                  bit_4.0.5

[7] doParallel_1.0.17                 lattice_0.22-5                    rjson_0.2.21

[10] evmix_2.12                        blob_1.2.4                        urlchecker_1.0.1

[13] S4Arrays_1.2.0                    seqLogo_1.68.0                    png_0.1-8

[16] ggplotify_0.1.2                   cli_3.6.2                         ProtGenerics_1.34.0

[19] goftest_1.2-3                     gargle_1.5.2                      BiocIO_1.12.0

[22] Signac_1.12.0                     stringdist_0.9.12                 uwot_0.1.16

[25] curl_5.2.0                        mime_0.12                         evaluate_0.23

[28] tidytree_0.4.6                    leiden_0.4.3.1                    stringi_1.8.3

[31] gsl_2.1-8                         XML_3.99-0.16                     httpuv_1.6.13

[34] AnnotationDbi_1.64.1              rappdirs_0.3.3                    splines_4.3.2

[37] RcppRoll_0.3.0                    DT_0.31                           sessioninfo_1.2.2

[40] DBI_1.1.3                         withr_2.5.2                       rprojroot_2.0.4

[43] lmtest_0.9-40                     tidygraph_1.2.3                   rtracklayer_1.62.0

[46] htmlwidgets_1.6.4                 fs_1.6.3                          biomaRt_2.58.0

[49] SingleCellExperiment_1.24.0       ggrepel_0.9.4                     SparseArray_1.2.2

[52] cellranger_1.1.0                  annotate_1.80.0                   reticulate_1.34.0

[55] zoo_1.8-12                        JASPAR2020_0.99.10                XVector_0.42.0

[58] knitr_1.45                        TFBSTools_1.40.0                  TFMPvalue_0.0.9

[61] timechange_0.2.0                  foreach_1.5.2                     fansi_1.0.6

[64] powerTCR_1.22.0                   caTools_1.18.2                    grid_4.3.2

[67] rhdf5_2.46.1                      vegan_2.6-4                       R.oo_1.25.0

[70] poweRlaw_0.70.6                   RSpectra_0.16-1                   irlba_2.3.5.1

[73] gridGraphics_0.5-1                fastDummies_1.7.3                 ellipsis_0.3.2

[76] lazyeval_0.2.2                    yaml_2.3.8                        ade4_1.7-22

[79] survival_3.5-7                    SpatialExperiment_1.12.0          scattermore_1.2

[82] BiocVersion_3.18.1                crayon_1.5.2                      RcppAnnoy_0.0.21

[85] progressr_0.14.0                  tweenr_2.0.2                      later_1.3.2

[88] ggridges_0.5.5                    codetools_0.2-19                  GlobalOptions_0.1.2

[91] profvis_0.3.8                     KEGGREST_1.42.0                   Rtsne_0.17

[94] shape_1.4.6                       Rsamtools_2.18.0                  filelock_1.0.3

[97] pkgconfig_2.0.3                   xml2_1.3.6                        GenomicAlignments_1.38.0

[100] aplot_0.2.2                       evd_2.3-6.1                       ape_5.7-1

[103] spatstat.sparse_3.0-3             BSgenome_1.70.1                   xtable_1.8-4

[106] plyr_1.8.9                        httr_1.4.7                        tools_4.3.2

[109] globals_0.16.2                    pkgbuild_1.4.3                    nlme_3.1-164

[112] dbplyr_2.4.0                      hdf5r_1.3.8                       ExperimentHub_2.10.0

[115] MatrixModels_0.5-3                shinyjs_2.1.0                     digest_0.6.33

[118] permute_0.9-7                     farver_2.1.1                      tzdb_0.4.0

[121] AnnotationFilter_1.26.0           reshape2_1.4.4                    yulab.utils_0.1.1

[124] DirichletMultinomial_1.44.0       glue_1.6.2                        cachem_1.0.8

[127] BiocFileCache_2.10.1              polyclip_1.10-6                   generics_0.1.3

[130] Biostrings_2.70.1                 ggalluvial_0.12.5                 googledrive_2.1.1

[133] parallelly_1.36.0                 pkgload_1.3.3                     RcppHNSW_0.5.0

[136] ScaledMatrix_1.10.0               pbapply_1.7-2                     spam_2.10-0

[139] utf8_1.2.4                        graphlayouts_1.0.2                gtools_3.9.5

[142] gridExtra_2.3                     shiny_1.8.0                       GenomeInfoDbData_1.2.11

[145] R.utils_2.12.3                    rhdf5filters_1.14.1               memoise_2.0.1

[148] rmarkdown_2.25                    R.methodsS3_1.8.2                 googlesheets4_1.1.1

[151] future_1.33.0                     RANN_2.6.1                        spatstat.data_3.0-3

[154] rstudioapi_0.15.0                 cluster_2.1.6                     spatstat.utils_3.0-4

[157] hms_1.1.3                         fitdistrplus_1.1-11               munsell_0.5.0

[160] colorspace_2.1-0                  rlang_1.1.2                       DelayedMatrixStats_1.24.0

[163] sparseMatrixStats_1.14.0          truncdist_1.0-2                   dotCall64_1.1-1

[166] shinydashboard_0.7.2              ggforce_0.4.1                     mgcv_1.9-0

[169] xfun_0.41                         CNEr_1.38.0                       iterators_1.0.14

[172] abind_1.4-5                       interactiveDisplayBase_1.40.0     EnsDb.Hsapiens.v86_2.99.0

[175] treeio_1.26.0                     Rhdf5lib_1.24.1                   bitops_1.0-7

[178] promises_1.2.1                    RSQLite_2.3.4                     DelayedArray_0.28.0

[181] GO.db_3.18.0                      compiler_4.3.2                    prettyunits_1.2.0

[184] beachmat_2.18.0                   listenv_0.9.0                     BSgenome.Hsapiens.UCSC.hg38_1.4.5

[187] AnnotationHub_3.10.0              BiocSingular_1.18.0               tensor_1.5

[190] MASS_7.3-60                       progress_1.2.3                    BiocParallel_1.36.0

[193] cubature_2.1.0                    spatstat.random_3.2-2             R6_2.5.1

[196] fastmap_1.1.1                     fastmatch_1.1-4                   ensembldb_2.26.0

[199] ROCR_1.0-11                       rsvd_1.0.5                        gtable_0.3.4

[202] KernSmooth_2.23-22                miniUI_0.1.1.1                    deldir_2.0-2

[205] htmltools_0.5.7                   bit64_4.0.5                       spatstat.explore_3.2-5

[208] lifecycle_1.0.4                   restfulr_0.0.15                   vctrs_0.6.5

[211] VGAM_1.1-9                        spatstat.geom_3.2-7               ggfun_0.1.3

[214] future.apply_1.11.0               pracma_2.4.4                      pillar_1.9.0

[217] GenomicFeatures_1.54.1            magick_2.8.1                      jsonlite_1.8.8

ncborcherding · 2023-12-19T13:01:51Z

Hey Harry,

Could you update to the newest scRepertoire version (v2.0.0)?

You can do this with:

devtools::install_github("ncborcherding/scRepertoire")

Some of the syntax and function names have been changed in the newest version, but StartracDiversity() has should work the same.

Nick

mainyanghr · 2023-12-20T20:40:35Z

Hey Harry,

Could you update to the newest scRepertoire version (v2.0.0)?

You can do this with:
devtools::install_github("ncborcherding/scRepertoire")
Some of the syntax and function names have been changed in the newest version, but StartracDiversity() has should work the same.

Nick

Thank you for kind help! I am not able to install the latest version.

devtools::install_github("ncborcherding/scRepertoire")
pkgbuild::check_build_tools(debug = TRUE)

Here comes the error messages;
Error: Failed to install 'scRepertoire' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

After debug:
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
sh: --version: command not found
using SDK: ‘NA’
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Warning messages:
1: In system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"), :
running command 'make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' compilers' had status 1
2: In system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
running command ''xcrun' --show-sdk-path 2>&1' had status 1

Error: Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

Thank you very much and have a great holidays.

ncborcherding · 2023-12-21T13:29:09Z

Hey Harry,

Looks like something is up with the ability to compile a package on your machine.

This post got a very similar error, might be worth reading.

I have tried the devtools call above as a fresh install on an M2 mac this morning and do not get the same error.

Nick

mainyanghr · 2023-12-21T14:12:06Z

Hey Harry,

Looks like something is up with the ability to compile a package on your machine.

This post got a very similar error, might be worth reading.

I have tried the devtools call above as a fresh install on an M2 mac this morning and do not get the same error.

Nick

Thank you very much. It is solved now by installing xcode-select --install in terminal.

ncborcherding · 2023-12-21T14:24:49Z

Thank you so much for the follow up on this and solution!

ncborcherding closed this as completed Dec 21, 2023

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StartracDiversity issue #290

StartracDiversity issue #290

mainyanghr commented Dec 18, 2023

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ncborcherding commented Dec 21, 2023

StartracDiversity issue #290

StartracDiversity issue #290

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mainyanghr commented Dec 18, 2023

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