rtracklayer
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20 hours ago •
lawremi
lawremi
error import bw file
Hi I am new to rtracklayer. Just install it from the github. But when I run the test code:
test_path <- system.file("tests", package = "rtracklayer")
test_bw <- file.path(test_path, "test.bw")
gr <- import(test_bw)
I got the following error:
Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (9) or length 1
I found people posting similar problem but no good answer https://support.bioconductor.org/p/9145565/
Below is my R info:
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
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-r0.3.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] 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] devtools_2.4.4 usethis_2.1.6 rtracklayer_1.57.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.3 IRanges_2.30.1
[7] S4Vectors_0.34.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] VGAM_1.1-7 colorspace_2.0-3 PureCN_2.2.0 rjson_0.2.21 ellipsis_0.3.2
[6] rprojroot_2.0.3 mclust_5.4.10 DNAcopy_1.70.0 futile.logger_1.4.3 XVector_0.36.0
[11] fs_1.5.2 rstudioapi_0.14 remotes_2.4.2 bit64_4.0.5 AnnotationDbi_1.58.0
[16] fansi_1.0.3 xml2_1.3.3 codetools_0.2-18 splines_4.2.1 cachem_1.0.6
[21] knitr_1.40 pkgload_1.3.0 Rsamtools_2.12.0 dbplyr_2.2.1 png_0.1-7
[26] shiny_1.7.2 compiler_4.2.1 httr_1.4.4 assertthat_0.2.1 Matrix_1.4-1
[31] fastmap_1.1.0 cli_3.3.0 later_1.3.0 formatR_1.12 htmltools_0.5.3
[36] prettyunits_1.1.1 tools_4.2.1 gtable_0.3.0 glue_1.6.2 GenomeInfoDbData_1.2.8
[41] dplyr_1.0.9 rappdirs_0.3.3 Rcpp_1.0.9 Biobase_2.56.0 vctrs_0.4.1
[46] Biostrings_2.64.1 rhdf5filters_1.8.0 xfun_0.32 stringr_1.4.1 ps_1.7.1
[51] mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.1 restfulr_0.0.15 XML_3.99-0.10
[56] zlibbioc_1.42.0 scales_1.2.1 BSgenome_1.64.0 VariantAnnotation_1.42.1 hms_1.1.2
[61] promises_1.2.0.1 MatrixGenerics_1.8.1 parallel_4.2.1 SummarizedExperiment_1.26.1 rhdf5_2.40.0
[66] lambda.r_1.2.4 RColorBrewer_1.1-3 yaml_2.3.5 curl_4.3.2 memoise_2.0.1
[71] gridExtra_2.3 ggplot2_3.3.6 biomaRt_2.52.0 stringi_1.7.8 RSQLite_2.2.16
[76] BiocIO_1.6.0 GenomicFeatures_1.48.3 filelock_1.0.2 pkgbuild_1.3.1 BiocParallel_1.30.3
[81] rlang_1.0.4 pkgconfig_2.0.3 matrixStats_0.62.0 bitops_1.0-7 evaluate_0.16
[86] lattice_0.20-45 purrr_0.3.4 Rhdf5lib_1.18.2 htmlwidgets_1.5.4 GenomicAlignments_1.32.1
[91] bit_4.0.4 tidyselect_1.1.2 processx_3.7.0 magrittr_2.0.3 R6_2.5.1
[96] profvis_0.3.7 generics_0.1.3 DelayedArray_0.22.0 DBI_1.1.3 withr_2.5.0
[101] pillar_1.8.1 KEGGREST_1.36.3 RCurl_1.98-1.8 tibble_3.1.8 crayon_1.5.1
[106] futile.options_1.0.1 utf8_1.2.2 BiocFileCache_2.4.0 urlchecker_1.0.1 rmarkdown_2.16
[111] progress_1.2.2 grid_4.2.1 data.table_1.14.2 blob_1.2.3 callr_3.7.2
[116] digest_0.6.29 xtable_1.8-4 httpuv_1.6.5 munsell_0.5.0 sessioninfo_1.2.2
Thanks in advance for your help.
Best
Forgot to mention, I am running the above command in my linux box in Rstudio
Please install the version from Bioconductor using BiocManager, which will also help you update all of your packages. If you still get the error, then please post a stack trace to help us figure this out.
Hey @lawremi, I sent the original post in support.bioconductor.org mentioned above, but let it rest in the meantime.
Here are the details with an up-to-date R 4.2.2, Bioconductor 3.16, rtracklayer 1.58.0, running the first import.bw example:
import.bw call
library('rtracklayer')
test_path <- system.file("tests", package = "rtracklayer")
test_bw <- file.path(test_path, "test.bw")
import.bw(test_bw)
Output:
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (9) or length 1
traceback()
11: stop(wmsg(what, " must have the length of the object ", "to construct (",
ans_len, ") or length 1"))
10: stop_if_wrong_length(what, ans_len)
9: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges,
strand = strand, mcols = mcols, seqinfo = seqinfo)
8: GRanges(rep(seqnames(which), nhits), C_ans[[1L]], seqinfo = si)
7: .local(con, format, text, ...)
6: import(FileForFormat(con, format), ...)
5: import(FileForFormat(con, format), ...)
4: import(con, "BigWig", ...)
3: import(con, "BigWig", ...)
2: import.bw(test_bw)
1: import.bw(test_bw)
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.11.0
LAPACK: /usr/lib/liblapack.so.3.11.0
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] rtracklayer_1.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.6 IRanges_2.32.0 S4Vectors_0.36.1
[6] BiocGenerics_0.44.0 colorout_1.2-2
loaded via a namespace (and not attached):
[1] XVector_0.38.0 zlibbioc_1.44.0 GenomicAlignments_1.34.0 BiocParallel_1.32.5
[5] lattice_0.20-45 rjson_0.2.21 tools_4.2.2 grid_4.2.2
[9] SummarizedExperiment_1.28.0 parallel_4.2.2 Biobase_2.58.0 matrixStats_0.63.0
[13] yaml_2.3.6 crayon_1.5.2 BiocIO_1.8.0 Matrix_1.5-3
[17] GenomeInfoDbData_1.2.9 restfulr_0.0.15 bitops_1.0-7 codetools_0.2-18
[21] RCurl_1.98-1.9 DelayedArray_0.24.0 compiler_4.2.2 MatrixGenerics_1.10.0
[25] Biostrings_2.66.0 Rsamtools_2.14.0 XML_3.99-0.13
The other tests run without problem:
rtracklayer:::.test()
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Timing stopped at: 0.056 0 0.057
Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (9) or length 1
In addition: Warning messages:
1: Use BiocIO::FileForFormat
2: Use BiocIO::FileForFormat
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
For efficiency, consider converting this WIG file to a BigWig file;
see ?wigToBigWig
RUNIT TEST PROTOCOL -- Fri Jan 20 01:32:59 2023
***********************************************
Number of test functions: 11
Number of errors: 1
Number of failures: 0
1 Test Suite :
rtracklayer RUnit Tests - 11 test functions, 1 error, 0 failures
ERROR in test_bw: Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (9) or length 1
Test files with failing tests
test_bw.R
test_bw
Error in BiocGenerics:::testPackage("rtracklayer") :
unit tests failed for package rtracklayer
In addition: There were 14 warnings (use warnings() to see them)
