Error: when using command "summary_trinotate(x)", an error occurred. #815

[pshdong]

Hi there

Downloading and installing package is fine, and loading the Trinotate annotation report is OK too.

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)'

> x <- read_trinotate(``"trinotate_annotation_report.xls"``)
Read 271320 rows and 17 (of 17) columns from 1.953 GB file in 00:00:36

> head(x, 2)
gene_id transcript_id sprot_Top_BLASTX_hit 1: TR100000|c0_g1 TR100000|c0_g1_i1 NA 2: TR100001|c0_g1 TR100001|c0_g1_i1 NA TrEMBL_Top_BLASTX_hit 1: NA 2: F6JS42_ERISI^F6JS42_ERISI^Q:254-6,H:30-112^74.7%ID^E:1e-40^.^.``X2C306_PROCL^X2C306_PROCL^Q:254-6,H:30-112^56.63%ID^E:9e-27^.^.``A2I7J2_PORPE^A2I7J2_PORPE^Q:251-6,H:31-112^52.44%ID^E:7e-23^SubName: Full=C-type lectin receptor {ECO:0000313|EMBL:ABM65757.1};^Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Brachyura; Eubrachyura; Portunoidea; Portunidae; Portunus RNAMMER prot_id prot_coords sprot_Top_BLASTP_hit TrEMBL_Top_BLASTP_hit Pfam SignalP 1: NA NA NA NA NA NA NA 2: NA NA NA NA NA NA NA TmHMM eggnog gene_ontology_blast gene_ontology_pfam transcript peptide 1: NA NA NA NA NA NA 2: NA NA NA NA NA NA

But when using command summary_trinotate(x), ends up with an error as below:

> summary_trinotate(x)
Error in forderv(x, by = by, retGrp = TRUE) : Failed to alloc cradix_counts

So, what is wrong?

[cstubben]

Sorry, the package is new and I have not tested on files larger than 80K rows, but it looks like data.table is failing on x1 <- x[,lapply(.SD, function(x) uniqueN(na.omit(x)) ),] or the next line in summary_trinotate.
I just updated read_trinotate so you can add an nrows option. Can you try the new function and set nrows=50000 and see if it still returns the error? I will also test on larger files here, but may take a few days before I have time.