Comments (3)
Impossible to know with that little information.
E.g.,
- Does it work if you process 1 sample?
- What version of bsseq?
- What's the output of
BiocManager::valid()
andsessionInfo()
? - What species and methylation context are you processing?
from bsseq.
1.Error reporting has not gone away if I process 1 sample.
2. bsseq’ version 1.30.0
4. human,
- BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://mirrors.ustc.edu.cn/CRAN/
- sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] bsseq_1.30.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 MatrixGenerics_1.6.0
[5] matrixStats_0.61.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[9] S4Vectors_0.32.4 BiocGenerics_0.40.0 methylSig_1.7.0 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] pkgload_1.2.4 splines_4.1.1 R.utils_2.11.0 DelayedMatrixStats_1.16.0
[5] gtools_3.9.2 brio_1.1.3 Rsamtools_2.10.0 BSgenome_1.62.0
[9] GenomeInfoDbData_1.2.7 yaml_2.3.5 remotes_2.4.2 sessioninfo_1.2.2
[13] lattice_0.20-45 glue_1.6.2 limma_3.50.1 XVector_0.34.0
[17] colorspace_2.0-3 R.oo_1.24.0 Matrix_1.4-1 XML_3.99-0.9
[21] devtools_2.4.3 DSS_2.42.0 zlibbioc_1.40.0 purrr_0.3.4
[25] scales_1.1.1 processx_3.5.3 HDF5Array_1.22.1 BiocParallel_1.28.3
[29] usethis_2.1.5 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0
[33] cli_3.2.0 magrittr_2.0.3 crayon_1.5.1 memoise_2.0.1
[37] ps_1.6.0 R.methodsS3_1.8.1 fs_1.5.2 pkgbuild_1.3.1
[41] tools_4.1.1 data.table_1.14.2 prettyunits_1.1.1 BiocIO_1.4.0
[45] lifecycle_1.0.1 Rhdf5lib_1.16.0 munsell_0.5.0 locfit_1.5-9.5
[49] DelayedArray_0.20.0 callr_3.7.0 Biostrings_2.62.0 compiler_4.1.1
[53] rlang_1.0.2 rhdf5_2.38.1 grid_4.1.1 RCurl_1.98-1.6
[57] rhdf5filters_1.6.0 rstudioapi_0.13 rjson_0.2.21 bitops_1.0-7
[61] testthat_3.1.3 restfulr_0.0.13 curl_4.3.2 R6_2.5.1
[65] GenomicAlignments_1.30.0 rtracklayer_1.54.0 fastmap_1.1.0 rprojroot_2.0.3
[69] permute_0.9-7 desc_1.4.1 parallel_4.1.1 Rcpp_1.0.8.3
[73] sparseMatrixStats_1.6.0
Bioconductor version '3.14'
- 0 packages out-of-date
- 1 packages too new
create a valid installation with
BiocManager::install("methylSig", update = TRUE, ask = FALSE)
more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] bsseq_1.30.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 MatrixGenerics_1.6.0
[5] matrixStats_0.61.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[9] S4Vectors_0.32.4 BiocGenerics_0.40.0 methylSig_1.7.0 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] pkgload_1.2.4 splines_4.1.1 R.utils_2.11.0 DelayedMatrixStats_1.16.0
[5] gtools_3.9.2 brio_1.1.3 Rsamtools_2.10.0 BSgenome_1.62.0
[9] GenomeInfoDbData_1.2.7 yaml_2.3.5 remotes_2.4.2 sessioninfo_1.2.2
[13] lattice_0.20-45 glue_1.6.2 limma_3.50.1 XVector_0.34.0
[17] colorspace_2.0-3 R.oo_1.24.0 Matrix_1.4-1 XML_3.99-0.9
[21] devtools_2.4.3 DSS_2.42.0 zlibbioc_1.40.0 purrr_0.3.4
[25] scales_1.1.1 processx_3.5.3 HDF5Array_1.22.1 BiocParallel_1.28.3
[29] usethis_2.1.5 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0
[33] cli_3.2.0 magrittr_2.0.3 crayon_1.5.1 memoise_2.0.1
[37] ps_1.6.0 R.methodsS3_1.8.1 fs_1.5.2 pkgbuild_1.3.1
[41] tools_4.1.1 data.table_1.14.2 prettyunits_1.1.1 BiocIO_1.4.0
[45] lifecycle_1.0.1 Rhdf5lib_1.16.0 munsell_0.5.0 locfit_1.5-9.5
[49] DelayedArray_0.20.0 callr_3.7.0 Biostrings_2.62.0 compiler_4.1.1
[53] rlang_1.0.2 rhdf5_2.38.1 grid_4.1.1 RCurl_1.98-1.6
[57] rhdf5filters_1.6.0 rstudioapi_0.13 rjson_0.2.21 bitops_1.0-7
[61] testthat_3.1.3 restfulr_0.0.13 curl_4.3.2 R6_2.5.1
[65] GenomicAlignments_1.30.0 rtracklayer_1.54.0 fastmap_1.1.0 rprojroot_2.0.3
[69] permute_0.9-7 desc_1.4.1 parallel_4.1.1 Rcpp_1.0.8.3
[73] sparseMatrixStats_1.6.0
from bsseq.
If you share an example file rather than a screenshot it'll be easier to help you
from bsseq.
Related Issues (20)
- BSmooth.tstat error, Error in compute.correction HOT 5
- read.bismark() too slow - input format issue? HOT 8
- BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment HOT 2
- Is it possible to append metadata to the GRanges within BSseq objects? HOT 3
- Normalization of the WGBS smooth data HOT 5
- bsseq incompatible with tictoc library HOT 1
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- read.bismark: option to change tmpdir in fread? HOT 4
- BSmooth with HDF5 realization backend error: Stop worker failed with the error: wrong args for environment subassignment HOT 5
- combineList: BACKEND Argument not working as intended HOT 1
- BSmooth.tstat issue HOT 11
- Updating beachmat to tatami HOT 1
- combine(sample1.smooth, sample2.smooth) gives in unsmooth results? HOT 4
- bsmooth() fails - Error in `h()`: ! error in evaluating the argument 'seed' in selecting a method for function 'DelayedArray': HDF5. File accessibility. Unable to open file. HOT 3
- Reading H5 files directly HOT 3
- error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark. HOT 26
- Represent a CpG with single row during import HOT 11
- exclude "Y" chromosome from bsseq object HOT 3
- Upcoming change to DelayedArray::realize() HOT 2
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from bsseq.