HicDCplus error, R_Reprotect: only 4 protected items, can't reprotect index -1 (from gi_list_write)
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gamma.jian ▴ 10
@franceschinigianmarco-16472
Last seen 10 weeks ago
Switzerland

Good morning, I am trying to apply HicDCPlus to a set of samples following the vignette code. However, I often get the following error when processing bigger chromosomes:

Chromosome chr1 complete.
Error in gi_list_write(gi_list, fname = output_path) :
  R_Reprotect: only 4 protected items, can't reprotect index -1

I tried to substitute the tmp folder with a local stable folder, but that did not solve the issue completely. Notice that I have installed the package from bitbucket as I am using R 4.0.2.

From my understanding, this has to do with the allocation of space for temporary files, but I haven't been able to understand this further. Any clue of what's going on?

Thank you

Here is my session info


sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /mnt/pd2/gianmarco/miniconda3/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.58.0
 [3] rtracklayer_1.50.0                Biostrings_2.58.0
 [5] XVector_0.30.0                    GenomicRanges_1.42.0
 [7] GenomeInfoDb_1.26.7               IRanges_2.24.1
 [9] S4Vectors_0.28.1                  BiocGenerics_0.36.1
[11] HiCDCPlus_0.99.14                 data.table_1.14.2
[13] forcats_0.5.1                     stringr_1.4.0
[15] dplyr_1.0.7                       purrr_0.3.4
[17] readr_2.1.1                       tidyr_1.1.4
[19] tibble_3.1.6                      ggplot2_3.3.5
[21] tidyverse_1.3.1

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2            ellipsis_0.3.2
  [3] htmlTable_2.3.0             biovizBase_1.38.0
  [5] base64enc_0.1-3             fs_1.5.2
  [7] dichromat_2.0-0             rstudioapi_0.13
  [9] bit64_4.0.5                 AnnotationDbi_1.52.0
 [11] fansi_0.5.0                 lubridate_1.8.0
 [13] xml2_1.3.3                  splines_4.0.2
 [15] R.methodsS3_1.8.1           cachem_1.0.6
 [17] knitr_1.36                  Formula_1.2-4
 [19] jsonlite_1.7.2              Rsamtools_2.6.0
 [21] broom_0.7.10                cluster_2.1.2
 [23] dbplyr_2.1.1                png_0.1-7
 [25] R.oo_1.24.0                 compiler_4.0.2
 [27] httr_1.4.2                  backports_1.4.0
 [29] lazyeval_0.2.2              assertthat_0.2.1
 [31] Matrix_1.4-0                fastmap_1.1.0
 [33] cli_3.1.0                   htmltools_0.5.2
 [35] prettyunits_1.1.1           tools_4.0.2
 [37] igraph_1.2.9                gtable_0.3.0
 [39] glue_1.5.1                  GenomeInfoDbData_1.2.4
 [41] rappdirs_0.3.3              Rcpp_1.0.7
 [43] Biobase_2.50.0              cellranger_1.1.0
 [45] vctrs_0.3.8                 xfun_0.28
 [47] librarian_1.8.1             rvest_1.0.2
 [49] lifecycle_1.0.1             ensembldb_2.14.1
 [51] XML_3.99-0.8                InteractionSet_1.18.1
 [53] MASS_7.3-54                 zlibbioc_1.36.0
 [55] scales_1.1.1                VariantAnnotation_1.36.0
 [57] ProtGenerics_1.22.0         GenomicInteractions_1.24.0
 [59] hms_1.1.1                   MatrixGenerics_1.2.1
 [61] SummarizedExperiment_1.20.0 AnnotationFilter_1.14.0
 [63] RColorBrewer_1.1-2          curl_4.3.2
 [65] gridExtra_2.3               memoise_2.0.1
 [67] rpart_4.1-15                biomaRt_2.46.3
 [69] latticeExtra_0.6-29         stringi_1.7.6
 [71] RSQLite_2.2.9               checkmate_2.0.0
 [73] GenomicFeatures_1.42.3      BiocParallel_1.24.1
 [75] rlang_0.4.12                pkgconfig_2.0.3
 [77] matrixStats_0.61.0          bitops_1.0-7
 [79] lattice_0.20-45             htmlwidgets_1.5.4
 [81] GenomicAlignments_1.26.0    bit_4.0.4
 [83] tidyselect_1.1.1            magrittr_2.0.1
 [85] R6_2.5.1                    generics_0.1.1
 [87] Hmisc_4.6-0                 DelayedArray_0.16.3
 [89] DBI_1.1.1                   foreign_0.8-81
 [91] pillar_1.6.4                haven_2.4.3
 [93] withr_2.4.3                 nnet_7.3-16
 [95] survival_3.2-13             RCurl_1.98-1.5
 [97] modelr_0.1.8                crayon_1.4.2
 [99] utf8_1.2.2                  BiocFileCache_1.14.0
[101] tzdb_0.2.0                  jpeg_0.1-9
[103] progress_1.2.2              grid_4.0.2
[105] readxl_1.3.1                blob_1.2.2
[107] reprex_2.0.1                digest_0.6.29
[109] R.utils_2.11.0              openssl_1.4.5
[111] munsell_0.5.0               Gviz_1.34.1
[113] askpass_1.1
hicd HiCDCPlus • 1.3k views
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0
Entering edit mode

If you cannot use HiCDCPlus available through Bioconductor distributions, you should be using the HiCDCPlus package from its GitHub source.

To do that, you can simply install devtools from CRAN and install from this GitHub repo:

install.packages("devtools") and then devtools::install_github("mervesa/HiCDCPlus")

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0
Entering edit mode

I also experience the same issue when trying to save the results with gi_list_write.

Error in gi_list_write(gi_list, fname = paste0(outdir, "/res_hicdicplus.txt")) : 
  R_Reprotect: only -2 protected items, can't reprotect index -7

sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] data.table_1.14.8                 BSgenome.Hsapiens.UCSC.hg38_1.4.4
 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.64.0
 [5] rtracklayer_1.56.1                Biostrings_2.64.1
 [7] XVector_0.36.0                    GenomicRanges_1.48.0
 [9] GenomeInfoDb_1.32.4               IRanges_2.30.1
[11] S4Vectors_0.34.0                  BiocGenerics_0.42.0
[13] HiCDCPlus_1.4.2
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