Comments (3)
I'd need to see some example code and data that I can use to reproduce the problem. Provide that, and I'll be happy to take a look. Also, pasting the output of sessionInfo()
would be helpful!
from sciclone.
I meet the same problem when running run.R
in manuscript/data/figure3 with data provided by https://github.com/genome/sciclone-meta and here is the output of my sessionInfo()
result.
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS/LAPACK: /home/ninomoriaty/anaconda3/envs/EvolCancer/lib/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] sciClone_1.1.0 TeachingDemos_2.10 MKmisc_1.6 plotrix_3.7-6 RColorBrewer_1.1-2 rgl_0.100.30
[7] bmm_0.3.1 NORMT3_1.0-3 ggplot2_3.2.1 IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 RSQLite_2.1.2 AnnotationDbi_1.46.1
[4] htmlwidgets_1.5.1 BiocParallel_1.18.1 pdp_0.7.0
[7] devtools_2.2.1 munsell_0.5.0 miniUI_0.1.1.1
[10] withr_2.1.2 colorspace_1.4-1 GOSemSim_2.10.0
[13] Biobase_2.44.0 knitr_1.25 rstudioapi_0.10
[16] robustbase_0.93-5 DOSE_3.10.2 labeling_0.3
[19] urltools_1.7.3 GenomeInfoDbData_1.2.1 polyclip_1.10-0
[22] bit64_0.9-7 farver_1.1.0 rprojroot_1.3-2
[25] vctrs_0.2.0 xfun_0.10 timescape_1.8.0
[28] R6_2.4.0 GenomeInfoDb_1.20.0 graphlayouts_0.5.0
[31] manipulateWidget_0.10.0 bitops_1.0-6 fgsea_1.10.1
[34] gridGraphics_0.4-1 DelayedArray_0.10.0 assertthat_0.2.1
[37] promises_1.1.0 scales_1.0.0 ggraph_2.0.0
[40] enrichplot_1.4.0 gtable_0.3.0 processx_3.4.1
[43] tidygraph_1.1.2 rlang_0.4.1 zeallot_0.1.0
[46] splines_3.6.1 rtracklayer_1.44.4 lazyeval_0.2.2
[49] europepmc_0.3 checkmate_1.9.4 BiocManager_1.30.9
[52] reshape2_1.4.3 crosstalk_1.0.0 backports_1.1.5
[55] httpuv_1.5.2 Meskit_0.1.0 qvalue_2.16.0
[58] clusterProfiler_3.12.0 tools_3.6.1 usethis_1.5.1
[61] ggplotify_0.0.4 ellipsis_0.3.0 sessioninfo_1.1.1
[64] ggridges_0.5.1 Rcpp_1.0.2 plyr_1.8.4
[67] progress_1.2.2 zlibbioc_1.30.0 purrr_0.3.3
[70] RCurl_1.95-4.12 ps_1.3.0 prettyunits_1.0.2
[73] viridis_0.5.1 cowplot_1.0.0 SummarizedExperiment_1.14.1
[76] ggrepel_0.8.1 fs_1.3.1 magrittr_1.5
[79] data.table_1.12.6 DO.db_2.9 triebeard_0.3.0
[82] reactome.db_1.68.0 matrixStats_0.55.0 pkgload_1.0.2
[85] hms_0.5.1 mime_0.7 xtable_1.8-4
[88] XML_3.98-1.20 gridExtra_2.3 testthat_2.2.1
[91] compiler_3.6.1 tibble_2.1.3 crayon_1.3.4
[94] BSgenome.Hsapiens.UCSC.hg19_1.4.0 htmltools_0.4.0 later_1.0.0
[97] tidyr_1.0.0 ReactomePA_1.28.0 DBI_1.0.0
[100] tweenr_1.0.1 corrplot_0.84 MASS_7.3-51.4
[103] rappdirs_0.3.1 Matrix_1.2-17 cli_1.1.0
[106] igraph_1.2.4.1 GenomicRanges_1.36.1 pkgconfig_2.0.3
[109] rvcheck_0.1.5 GenomicAlignments_1.20.1 xml2_1.2.2
[112] webshot_0.5.1 XVector_0.24.0 clonevol_0.99.11
[115] stringr_1.4.0 callr_3.3.2 digest_0.6.22
[118] graph_1.62.0 Biostrings_2.52.0 fastmatch_1.1-0
[121] curl_4.2 shiny_1.4.0 Rsamtools_2.0.3
[124] graphite_1.30.0 lifecycle_0.1.0 nlme_3.1-141
[127] jsonlite_1.6 desc_1.2.0 viridisLite_0.3.0
[130] limma_3.40.6 BSgenome_1.52.0 pillar_1.4.2
[133] ggsci_2.9 lattice_0.20-38 deconstructSigs_1.8.0
[136] fastmap_1.0.1 httr_1.4.1 DEoptimR_1.0-8
[139] pkgbuild_1.0.6 GO.db_3.8.2 glue_1.3.1
[142] remotes_2.1.0 UpSetR_1.4.0 fishplot_0.5
[145] bit_1.1-14 ggforce_0.3.1 stringi_1.4.3
[148] blob_1.2.0 memoise_1.1.0 dplyr_0.8.3
[151] ape_5.3
Thank you for your attention and we will be grateful for your reply.
Wang Chengwei
from sciclone.
After simply testing, I found that this line in function sc.plot2dWithMargins
may cause the problem:
max.density <- max(tmp[["data"]][[1]]$ymax)
As the variable ymax is set to be NULL and tmp[["data"]][[1]] seems to be a vector, it may lead to the error:
Error: $ operator is invalid for atomic vectors
However, I meet another problem caused by downViewport('panel.3-4-3-4')
and the error is :
Error in grid.Call.graphics(C_downviewport, name$name, strict) :
Viewport 'panel.3-4-3-4' was not found
This error confuses me as it seems that panel.3-4-3-4
appears only once and I don't know how to check it. I would be really thankful if there are any technical solutions provided.
Wang Chengwei
from sciclone.
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