Entering edit mode
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
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")
I also experience the same issue when trying to save the results with
gi_list_write
.