Error while using GenomicFeatures package
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TFony ▴ 10
@tfony-12313
Last seen 4.6 years ago

Hi guys;

I get a problem when I build txdb obejctes using makeTxDbFromGFF

 

> file.exists("Homo_sapiens.GRCh38.87.gtf")

[1] TRUE

> txdb <- makeTxDbFromGFF("Homo_sapiens.GRCh38.87.gtf",format = "gtf",circ_seqs = character())

Import genomic features from the file as a GRanges object ...

It stuck here for a long time. There is no further progess.

It's an bug for linux's R? Thanks for any help!!!!!!

 

> sessionInfo()

R version 3.2.0 (2015-04-16)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.5 LTS

 

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

 

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets

[8] methods   base

 

other attached packages:

[1] GenomicFeatures_1.20.6 AnnotationDbi_1.30.1   Biobase_2.28.0

[4] GenomicRanges_1.20.8   GenomeInfoDb_1.4.3     IRanges_2.2.9

[7] S4Vectors_0.6.6        BiocGenerics_0.14.0

 

loaded via a namespace (and not attached):

 [1] XML_3.98-1.2            Rsamtools_1.20.5        Biostrings_2.36.4

 [4] GenomicAlignments_1.4.2 bitops_1.0-6            futile.options_1.0.0

 [7] DBI_0.3.1               RSQLite_1.0.0           zlibbioc_1.14.0

[10] XVector_0.8.0           futile.logger_1.4.3     lambda.r_1.1.9

[13] BiocParallel_1.2.22     tools_3.2.0             biomaRt_2.24.1

[16] RCurl_1.95-4.6          rtracklayer_1.28.10

genomicfeatures maketxdbfromgff • 615 views
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Hi,

You're using BioC 3.1, which is 2 year old and not supported anymore. Please update to the current Bioconductor release, BioC 3.4, which requires R 3.3. makeTxDbFromGFF() has been significantly improved in the last couple of years. In particular, it's faster and more memory efficient than it used to be.

Cheers,

H.

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Thanks for your help. It works while everthing is updated.
 

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