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Hello,
I got the error while using forgeBSgenomeDataPkg during TwoBits_export since the inst directory is not creating. Please check the following comand output of forgeBSgenomeDataPkg, taceback, sessioninfo and zzz.r file
packageVersion("BSgenome")
[1] ‘1.52.0’
forgeBSgenomeDataPkg("oindicaseed.txt")
Creating package in ./BSgenome.Oindica.ASM465v1
Loading '1' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr1.fa' ... DONE
Loading '2' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr2.fa' ... DONE
Loading '3' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr3.fa' ... DONE
Loading '4' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr4.fa' ... DONE
Loading '5' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr5.fa' ... DONE
Loading '6' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr6.fa' ... DONE
Loading '7' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr7.fa' ... DONE
Loading '8' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr8.fa' ... DONE
Loading '9' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr9.fa' ... DONE
Loading '10' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr10.fa' ... DONE
Loading '11' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr11.fa' ... DONE
Loading '12' sequence from FASTA file '/home/ns43567/CEIB_rice_project/JHI/ensembl_indica/split_chromosome/outroot/chr12.fa' ... DONE
Writing all sequences to './BSgenome.Oindica.ASM465v1/inst/extdata/single_sequences.2bit' ... Error in .TwoBits_export(mapply(.DNAString_to_twoBit, object, seqnames), :
UCSC library operation failed
In addition: Warning messages:
1: In readLines(infile, n = 25000L) :
incomplete final line found on 'oindicaseed.txt'
2: In .TwoBits_export(mapply(.DNAString_to_twoBit, object, seqnames), :
mustOpen: Can't open ./BSgenome.Oindica.ASM465v1/inst/extdata/single_sequences.2bit to write: No such file or directory
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /mnt/du-synology/v1shr1/scratch/ns43567/apps/conda/lib/libopenblasp-r0.3.7.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BSgenome_1.52.0 rtracklayer_1.44.3 Biostrings_2.52.0
[4] XVector_0.24.0 GenomicRanges_1.36.0 GenomeInfoDb_1.20.0
[7] IRanges_2.18.2 S4Vectors_0.22.0 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] matrixStats_0.54.0 lattice_0.20-38
[3] XML_3.98-1.20 Rsamtools_2.0.0
[5] GenomicAlignments_1.20.1 bitops_1.0-6
[7] grid_3.6.1 zlibbioc_1.30.0
[9] Matrix_1.2-17 BiocParallel_1.18.1
[11] tools_3.6.1 Biobase_2.44.0
[13] RCurl_1.95-4.12 DelayedArray_0.10.0
[15] compiler_3.6.1 SummarizedExperiment_1.14.1
[17] GenomeInfoDbData_1.2.1
traceback()
14: .TwoBits_export(mapply(.DNAString_to_twoBit, object, seqnames),
twoBitPath(path(con)))
13: .local(object, con, format, ...)
12: export(object, FileForFormat(con, format), ...)
11: export(object, FileForFormat(con, format), ...)
10: export(seqs, dest_filepath, format = "2bit")
9: export(seqs, dest_filepath, format = "2bit")
8: .forgeTwobitFileFromFastaFiles(seqnames, prefix, suffix, seqs_srcdir,
seqs_destdir, verbose = verbose)
7: forgeSeqFiles(.seqnames, mseqnames = .mseqnames, seqfile_name = x@seqfile_name,
prefix = x@seqfiles_prefix, suffix = x@seqfiles_suffix, seqs_srcdir = seqs_srcdir,
seqs_destdir = seqs_destdir, ondisk_seq_format = x@ondisk_seq_format,
verbose = verbose)
6: forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,
verbose = verbose)
5: forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,
verbose = verbose)
4: forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,
verbose = verbose)
3: forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, destdir = destdir,
verbose = verbose)
2: forgeBSgenomeDataPkg("oindicaseed.txt")
1: forgeBSgenomeDataPkg("oindicaseed.txt")
R/zzz.R file
.pkgname <- "BSgenome.Oindica.ASM465v1"
.seqnames <- paste(c(1:12), sep="")
.circ_seqs <- NULL
.mseqnames <- NULL
.onLoad <- function(libname, pkgname)
{
if (pkgname != .pkgname)
stop("package name (", pkgname, ") is not ",
"the expected name (", .pkgname, ")")
extdata_dirpath <- system.file("extdata", package=pkgname,
lib.loc=libname, mustWork=TRUE)
## Make and export BSgenome object.
bsgenome <- BSgenome(
organism="Oryza sativa indica",
common_name="rice",
provider="ensembl",
provider_version="v1",
release_date="2011",
release_name="ASM465v1",
source_url="ftp://ftp.ensemblgenomes.org/pub/plants/release-44/fasta/oryza_indica/dna/",
seqnames=.seqnames,
circ_seqs=.circ_seqs,
mseqnames=.mseqnames,
seqs_pkgname=pkgname,
seqs_dirpath=extdata_dirpath
)
ns <- asNamespace(pkgname)
objname <- pkgname
assign(objname, bsgenome, envir=ns)
namespaceExport(ns, objname)
old_objname <- "Oindica"
assign(old_objname, bsgenome, envir=ns)
namespaceExport(ns, old_objname)
}
Thank you verymuch.
Can you please show us the output of:
Thanks,
H.
Hi,
I am unable to get the tree command in our institute cluster. I am trying to install it in the local user but haven't succeded. Can I get any alternative command for the required information otherwise I will check with the admin and update here.
Thanks a lot!
Nagesh
Just do:
All we need to know is whether we see the
extdatasubfolder there. Theextdatasubfolder is an empty subfolder but it's important to have it there as it's part of the pkg template used to forge BSgenome data packages.I suspect you don't have the
extdatasubfolder, which would indicate that BSgenome was installed from an incorrect/incomplete source tarball. You see, a few years ago R core changed the behavior ofR CMD build: they decided that by defaultR CMD buildshould ignore the empty folders found in the package source tree. By doing so they brokeR CMD buildon all packages that rely on the presence of some empty folders in their directory structure in order to function properly. They decided that package developers should now use--keep-empty-dirsif they wantedR CMD buildto preserve the directory structure of their package. Problem is that package developers don't control what other people do to build package source tarballs. This is why the Bioconductor build system uses this option to build all package source tarballs (see https://bioconductor.org/checkResults/3.9/bioc-LATEST/BSgenome/malbec2-buildsrc.html).So let's see if it is the case that BSgenome was installed from a broken source tarball on your system.
H.