Dear Developers,
I got an initial error while running findDMRs.r
There were 50 or more warnings (use warnings() to see the first 50)
Warning messages:
1: In mclapply(1:nrow(X2), foo, mc.cores = ncores) :
scheduled core 138 did not deliver a result, all values of the job will be affected
2: In shrk.phi[ix] <- shrk.phi2 :
number of items to replace is not a multiple of replacement length
3: In mclapply(1:nrow(X2), foo, mc.cores = ncores) :
scheduled core 166 did not deliver a result, all values of the job will be affected
4: In shrk.phi[ix] <- shrk.phi2 :
number of items to replace is not a multiple of replacement length
Error in if (substr(level[i], 1, 3) == "chr") { :
argument is of length zero
Execution halted
Then as discussed in one of your issues, I edited the codes to run in R >4 version.
Then the tool gave me an output but with additional warnings. Should i be concerned?
Warning messages:
1: In mclapply(1:nrow(X2), foo, mc.cores = ncores) :
scheduled core 154 did not deliver a result, all values of the job will be affected
2: In shrk.phi[ix] <- shrk.phi2 :
number of items to replace is not a multiple of replacement length
sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.7 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /usr/local/intel/2024.0.1.46/mkl/2024.0/lib/libmkl_rt.so.2; LAPACK version 3.10.1
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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] Matrix_1.7-3 gtable_0.3.6
[3] jsonlite_2.0.0 dplyr_1.1.4
[5] compiler_4.5.0 renv_1.1.5
[7] crayon_1.5.3 tidyselect_1.2.1
[9] Rcpp_1.1.0 SummarizedExperiment_1.38.1
[11] Biobase_2.68.0 GenomicRanges_1.60.0
[13] parallel_4.5.0 IRanges_2.42.0
[15] scales_1.4.0 BiocParallel_1.42.1
[17] lattice_0.22-6 ggplot2_3.5.2
[19] R6_2.6.1 XVector_0.48.0
[21] S4Arrays_1.8.1 generics_0.1.4
[23] GenomeInfoDb_1.44.1 BiocGenerics_0.54.0
[25] tibble_3.3.0 DelayedArray_0.34.1
[27] MatrixGenerics_1.20.0 GenomeInfoDbData_1.2.14
[29] pillar_1.11.0 RColorBrewer_1.1-3
[31] rlang_1.1.6 SparseArray_1.8.1
[33] cli_3.6.5 magrittr_2.0.3
[35] locfit_1.5-9.12 grid_4.5.0
[37] lifecycle_1.0.4 DESeq2_1.48.1
[39] S4Vectors_0.49.0 vctrs_0.6.5
[41] glue_1.8.0 farver_2.1.2
[43] codetools_0.2-20 abind_1.4-8
[45] stats4_4.5.0 httr_1.4.7
[47] pkgconfig_2.0.3 matrixStats_1.5.0
[49] tools_4.5.0 UCSC.utils_1.4.0
Kindly guide me through.
Dear Developers,
I got an initial error while running findDMRs.r
There were 50 or more warnings (use warnings() to see the first 50)
Warning messages:
1: In mclapply(1:nrow(X2), foo, mc.cores = ncores) :
scheduled core 138 did not deliver a result, all values of the job will be affected
2: In shrk.phi[ix] <- shrk.phi2 :
number of items to replace is not a multiple of replacement length
3: In mclapply(1:nrow(X2), foo, mc.cores = ncores) :
scheduled core 166 did not deliver a result, all values of the job will be affected
4: In shrk.phi[ix] <- shrk.phi2 :
number of items to replace is not a multiple of replacement length
Error in if (substr(level[i], 1, 3) == "chr") { :
argument is of length zero
Execution halted
Then as discussed in one of your issues, I edited the codes to run in R >4 version.
Then the tool gave me an output but with additional warnings. Should i be concerned?
Warning messages:
1: In mclapply(1:nrow(X2), foo, mc.cores = ncores) :
scheduled core 154 did not deliver a result, all values of the job will be affected
2: In shrk.phi[ix] <- shrk.phi2 :
number of items to replace is not a multiple of replacement length
Matrix products: default
BLAS/LAPACK: /usr/local/intel/2024.0.1.46/mkl/2024.0/lib/libmkl_rt.so.2; LAPACK version 3.10.1
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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] Matrix_1.7-3 gtable_0.3.6
[3] jsonlite_2.0.0 dplyr_1.1.4
[5] compiler_4.5.0 renv_1.1.5
[7] crayon_1.5.3 tidyselect_1.2.1
[9] Rcpp_1.1.0 SummarizedExperiment_1.38.1
[11] Biobase_2.68.0 GenomicRanges_1.60.0
[13] parallel_4.5.0 IRanges_2.42.0
[15] scales_1.4.0 BiocParallel_1.42.1
[17] lattice_0.22-6 ggplot2_3.5.2
[19] R6_2.6.1 XVector_0.48.0
[21] S4Arrays_1.8.1 generics_0.1.4
[23] GenomeInfoDb_1.44.1 BiocGenerics_0.54.0
[25] tibble_3.3.0 DelayedArray_0.34.1
[27] MatrixGenerics_1.20.0 GenomeInfoDbData_1.2.14
[29] pillar_1.11.0 RColorBrewer_1.1-3
[31] rlang_1.1.6 SparseArray_1.8.1
[33] cli_3.6.5 magrittr_2.0.3
[35] locfit_1.5-9.12 grid_4.5.0
[37] lifecycle_1.0.4 DESeq2_1.48.1
[39] S4Vectors_0.49.0 vctrs_0.6.5
[41] glue_1.8.0 farver_2.1.2
[43] codetools_0.2-20 abind_1.4-8
[45] stats4_4.5.0 httr_1.4.7
[47] pkgconfig_2.0.3 matrixStats_1.5.0
[49] tools_4.5.0 UCSC.utils_1.4.0
Kindly guide me through.