Question: Importing transcript abundance datasets generated with Salmon 0.14.0
0
gravatar for edoardobertolini
14 days ago by
edoardobertolini0 wrote:

Hi! I have recently updated Salmon to the latest version (0.14.0) and I'm not anymore able to import Salmon outputs into R using the code

tximport(file, type = "salmon", txOut = TRUE, countsFromAbundance = "no")

This is the error that I get when I run the code above:

txi <- tximport(file, type = "salmon", txOut = TRUE, countsFromAbundance = "no") reading in files with read_tsv Error in readBin(bootCon, "integer", n = expected.n) : invalid 'n' argument

Any suggestion? Thanks

Edo

tximport • 75 views
ADD COMMENTlink modified 14 days ago by Michael Love24k • written 14 days ago by edoardobertolini0
Answer: Importing transcript abundance datasets generated with Salmon 0.14.0
0
gravatar for Michael Love
14 days ago by
Michael Love24k
United States
Michael Love24k wrote:

This was just fixed by Rory Kirchner, and we will propagate to release (1.12.1) and devel (1.13.3).

ADD COMMENTlink written 14 days ago by Michael Love24k

Getting the same error, is there any quick fix? Thanks ML for working on it.

ADD REPLYlink written 12 days ago by lech.kaczmarczyk10

It's fixed. What version are you using?

sessionInfo()
ADD REPLYlink written 12 days ago by Michael Love24k
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] tximport_1.13.3      biomaRt_2.41.3       matrixStats_0.54.0   data.table_1.12.2    pheatmap_1.0.12     
 [6] org.Mm.eg.db_3.8.2   AnnotationDbi_1.47.0 IRanges_2.19.9       S4Vectors_0.23.11    Biobase_2.45.0      
[11] BiocGenerics_0.31.4 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.15.1 progress_1.2.2              tidyselect_0.2.5           
 [4] purrr_0.3.2                 rhdf5_2.29.0                lattice_0.20-38            
 [7] colorspace_1.4-1            blob_1.1.1                  XML_3.98-1.20              
[10] rlang_0.3.4                 pillar_1.4.1                glue_1.3.1                 
[13] DBI_1.0.0                   BiocParallel_1.19.0         bit64_0.9-7                
[16] RColorBrewer_1.1-2          GenomeInfoDbData_1.2.1      stringr_1.4.0              
[19] zlibbioc_1.31.0             munsell_0.5.0               gtable_0.3.0               
[22] memoise_1.1.0               GenomeInfoDb_1.21.1         curl_3.3                   
[25] Rcpp_1.0.1                  readr_1.3.1                 scales_1.0.0               
[28] BiocManager_1.30.4          DelayedArray_0.11.0         jsonlite_1.6               
[31] XVector_0.25.0              bit_1.1-14                  hms_0.4.2                  
[34] digest_0.6.19               stringi_1.4.3               dplyr_0.8.1                
[37] GenomicRanges_1.37.10       grid_3.6.0                  tools_3.6.0                
[40] bitops_1.0-6                magrittr_1.5                RCurl_1.95-4.12            
[43] RSQLite_2.1.1               tibble_2.1.3                crayon_1.3.4               
[46] pkgconfig_2.0.2             Matrix_1.2-17               prettyunits_1.0.2          
[49] assertthat_0.2.1            httr_1.4.0                  rstudioapi_0.10            
[52] Rhdf5lib_1.7.2              R6_2.4.0                    compiler_3.6.0
ADD REPLYlink written 12 days ago by lech.kaczmarczyk10
1

Can you reload R and try the code again?

At least two others have reported that the new versions fix the bug.

ADD REPLYlink written 12 days ago by Michael Love24k
1

OK, I reinstalled it and now it's working! Thanks again Michael!

ADD REPLYlink written 12 days ago by lech.kaczmarczyk10
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