Error in e2[[j]]: subscript out of bounds

[RodrigoGM]

Hi qdnaseq team !
I'm running into some trouble while running callBins. I'm analyzing sparse DNA sequencing data and the combined data is a mixture of tumors with and w/o CNA. Is it how the data is being passed from callBins to CGHcall? or a bug in CGHcall?

any help would be most appreciated,

Error message is:

49 > cn100 <- cn100 %>%                                                                                                                                                           
50 +     callBins()                                                                                                                                                               
51 Dividing chromosomes into arms using centromere positions from GRCh37
52 
53 [1] 1
54 [1] 2
55 [1] 3
56 [1] 4
57 [1] 5
58 [1] 6
59 [1] 7
60 [1] 8
61 [1] 9
62 [1] 10
63 [1] 11
64 [1] 12
65 [1] 13
66 [1] 14
67 [1] 15
68 [1] 16
69 [1] 17
70 [1] 18
71 [1] 19
72 [1] 20
73 [1] 21
74 [1] 22
75 [1] 23
76 [1] 24
77 EM algorithm started ...
78 
79 Error: Command CGHcall() returned the following error message:
80 Error in e2[[j]]: subscript out of bounds
81 Please contact maintainer of package CGHcall: Mark van de Wiel <[email protected]>

Session Info

82  > sessionInfo()
83  R version 4.0.5 (2021-03-31)
84  Platform: x86_64-pc-linux-gnu (64-bit)
85  Running under: CentOS Linux 7 (Core)
86 
87  Matrix products: default
88  BLAS:   CentOS_7/R/R-4.0.5/lib64/R/lib/libRblas.so
89  LAPACK: CentOS_7/R/R-4.0.5/lib64/R/lib/libRlapack.so
90 
91  locale:
92   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
93   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
94   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
95   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
96   [9] LC_ADDRESS=C               LC_TELEPHONE=C
97  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
98 
99  attached base packages:
100 [1] parallel  stats     graphics  grDevices utils     datasets  methods
101 [8] base
102 
103 other attached packages:
104  [1] Biobase_2.50.0      BiocGenerics_0.36.1 forcats_0.5.1
105  [4] stringr_1.4.0       dplyr_1.0.7         purrr_0.3.4
106  [7] readr_2.0.1         tidyr_1.1.3         tibble_3.1.3
107 [10] ggplot2_3.3.5       tidyverse_1.3.0     QDNAseq_1.31.0
108 
109 loaded via a namespace (and not attached):
110  [1] httr_1.4.2             CGHcall_2.52.0         jsonlite_1.7.2
111  [4] R.utils_2.11.0         modelr_0.1.8           assertthat_0.2.1
112  [7] stats4_4.0.5           GenomeInfoDbData_1.2.4 cellranger_1.1.0
113 [10] Rsamtools_2.6.0        impute_1.64.0          globals_0.14.0
114 [13] pillar_1.6.2           backports_1.2.1        glue_1.4.2
115 [16] limma_3.46.0           digest_0.6.29          GenomicRanges_1.38.0
116 [19] XVector_0.30.0         rvest_1.0.0            colorspace_2.0-2
117 [22] R.oo_1.24.0            pkgconfig_2.0.3        broom_0.7.8
118 [25] listenv_0.8.0          haven_2.4.1            zlibbioc_1.36.0
119 [28] scales_1.1.1           tzdb_0.1.2             BiocParallel_1.24.1
120 [31] generics_0.1.0         IRanges_2.24.1         ellipsis_0.3.2
121 [34] withr_2.4.2            cli_3.0.1              magrittr_2.0.1
122 [37] crayon_1.5.0           readxl_1.3.1           R.methodsS3_1.8.1
123 [40] fs_1.5.0               future_1.24.0          fansi_0.5.0
124 [43] parallelly_1.30.0      xml2_1.3.2             tools_4.0.5

[HenrikBengtsson]

Thanks for the report. As the error message says, this might be something that the maintainer of the CGHcall package has to fix.

Having said that, can you please

saveRDS(cn100, "cn100.rds.zip")

and attach it here, so the error can be reproduced and investigated? The *.zip extension is to trick GitHub to accept the file.