kasperdanielhansen
commented
3 years ago I would not worry, but thanks a lot for alerting us to this. There much have been some (recent) changes in reading binary files, and we should fix this, either in minfi or (more likely) illuminaio.
Thanks, Kasper
On Thu, Apr 8, 2021 at 3:49 PM orzechoj @.***> wrote:
Hi,
I'm getting these warnings when I read data
RGSet <- read.metharray.exp(targets = targets) Warning in readChar(con, nchars = n): truncating string with embedded nuls Warning in readChar(con, nchars = n): truncating string with embedded nuls Warning in readChar(con, nchars = n): truncating string with embedded nuls .. . ..
It seems as this is a quite common problem, since it's mini user guide too: https://bioconductor.org/packages/release/bioc/vignettes/minfi/inst/doc/minfi.html
The GenomicRatioSet object still looks ok, so should I worry about this?
Session details below:
sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /sw/apps/R/x86_64/4.0.0/rackham/lib64/R/lib/libRblas.so LAPACK: /sw/apps/R/x86_64/4.0.0/rackham/lib64/R/lib/libRlapack.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=sv_SE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] minfi_1.34.0 bumphunter_1.30.0 [3] locfit_1.5-9.4 iterators_1.0.12 [5] foreach_1.5.0 Biostrings_2.56.0 [7] XVector_0.28.0 SummarizedExperiment_1.18.2 [9] DelayedArray_0.14.1 matrixStats_0.56.0 [11] Biobase_2.48.0 GenomicRanges_1.40.0 [13] GenomeInfoDb_1.24.2 IRanges_2.22.2 [15] S4Vectors_0.26.1 BiocGenerics_0.34.0
loaded via a namespace (and not attached): [1] nlme_3.1-147 bitops_1.0-6 [3] bit64_0.9-7 RColorBrewer_1.1-2 [5] progress_1.2.2 httr_1.4.1 [7] tools_4.0.0 doRNG_1.8.2 [9] nor1mix_1.3-0 R6_2.4.1 [11] HDF5Array_1.16.0 DBI_1.1.0 [13] tidyselect_1.1.0 prettyunits_1.1.1 [15] base64_2.0 bit_1.1-15.2 [17] curl_4.3 compiler_4.0.0 [19] preprocessCore_1.50.0 xml2_1.3.2 [21] rtracklayer_1.48.0 readr_1.3.1 [23] genefilter_1.70.0 quadprog_1.5-8 [25] askpass_1.1 rappdirs_0.3.1 [27] stringr_1.4.0 digest_0.6.25 [29] Rsamtools_2.4.0 illuminaio_0.30.0 [31] siggenes_1.62.0 GEOquery_2.56.0 [33] pkgconfig_2.0.3 scrime_1.3.5 [35] dbplyr_1.4.3 limma_3.44.1 [37] rlang_0.4.8 RSQLite_2.2.0 [39] DelayedMatrixStats_1.10.0 generics_0.0.2 [41] mclust_5.4.6 BiocParallel_1.22.0 [43] dplyr_1.0.2 RCurl_1.98-1.2 [45] magrittr_1.5 GenomeInfoDbData_1.2.3 [47] Matrix_1.2-18 Rcpp_1.0.5 [49] Rhdf5lib_1.10.0 lifecycle_0.2.0 [51] stringi_1.4.6 MASS_7.3-51.6 [53] zlibbioc_1.34.0 rhdf5_2.32.0 [55] plyr_1.8.6 BiocFileCache_1.12.0 [57] grid_4.0.0 blob_1.2.1 [59] crayon_1.3.4 lattice_0.20-41 [61] splines_4.0.0 multtest_2.44.0 [63] GenomicFeatures_1.40.0 annotate_1.66.0 [65] hms_0.5.3 beanplot_1.2 [67] pillar_1.4.6 rngtools_1.5 [69] codetools_0.2-16 biomaRt_2.44.0 [71] XML_3.99-0.3 glue_1.4.2 [73] data.table_1.12.8 vctrs_0.3.4 [75] tidyr_1.1.2 openssl_1.4.1 [77] purrr_0.3.4 reshape_0.8.8 [79] assertthat_0.2.1 xtable_1.8-4 [81] survival_3.1-12 tibble_3.0.3 [83] GenomicAlignments_1.24.0 AnnotationDbi_1.50.0 [85] memoise_1.1.0 ellipsis_0.3.1
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-- Best, Kasper
Hi,
I'm getting these warnings when I read data
It seems as this is a quite common problem, since it's in the minfi user guide too: https://bioconductor.org/packages/release/bioc/vignettes/minfi/inst/doc/minfi.html
The GenomicRatioSet object still looks ok, so should I worry about this?
Session details below: