I'm trying to use tximport with salmon quantifications. Initially I had some problems installing tximport because of the version of R (3.3.1) and bioconductor (3.2) installed on our Rstudio server so (while I wait for the guys who maintain that to fix it) I figured I'd install it directly from the bioconductor github site:

library(devtools)
dev_mode(on=T)
install_github("Bioconductor-mirror/tximport")
install_github("hadley/readr")

This went just fine, but when I then try to load some data I get the following error:

library(tximport)
library(readr)
tximp_files <- file.path(exp[[3]], "quant.sf")
txi <- tximport(files, type="salmon", tx2gene=t2g)

reading in files with read_tsv
1 

Error in guess_header_(datasource, tokenizer, locale) : basic_string::resize

9.

stop(structure(list(message = "basic_string::resize", call = guess_header_(datasource, tokenizer, locale), cppstack = NULL), .Names = c("message", "call", "cppstack"), class = c("std::length_error", "C++Error", "error", "condition")))

8.

guess_header_(datasource, tokenizer, locale)

7.

guess_header(ds_header, tokenizer, locale)

6.

col_spec_standardise(data, skip = skip, comment = comment, guess_max = guess_max, col_names = col_names, col_types = col_types, tokenizer = tokenizer, locale = locale)

5.

read_delimited(file, tokenizer, col_names = col_names, col_types = col_types, locale = locale, skip = skip, comment = comment, n_max = n_max, guess_max = guess_max, progress = progress)

4.

readr::read_tsv(x, progress = FALSE, col_types = readr::cols())

3.

importer(files[i])

2.

as.data.frame(importer(files[i]))

1.

tximport(files, type = "salmon", tx2gene = t2g)

The quant.sf data were generated with salmon 0.5.1, the file paths are correct and the files look like:

# salmon (mapping-based) v0.5.1
# [ program ] => salmon 
# [ command ] => quant 
# [ index ] => { /Projects/Arabidopsis_annotations/TAIR10/ensembl/release_26/Sequence/SalmonIndex/transcripts_index_salmon0.5.1_quasi }
# [ libType ] => { ISR }
# [ mates1 ] => { /Projects/salmon/0.5.1_bootstraps/Col-1/R1.fastq }
# [ mates2 ] => { /Projects/salmon/0.5.1_bootstraps/Col-1/R2.fastq }
# [ output ] => { /Projects/salmon/0.5.1_bootstraps/Col-1/TAIR10 }
# [ threads ] => { 8 }
# [ numBootstraps ] => { 100 }
# [ mapping rate ] => { 66.1342% }
# Name    Length    TPM    NumReads
ATMG00010.1    462    1.99872    65
ATMG00030.1    324    4334.17    73792.3
ATMG00040.1    948    11.5158    1018.12
ATMG00050.1    396    0.551205    13.7941
ATMG00060.1    542    564.503    23531.1
ATMG00070.1    573    318.244    14399.1

If you already have mis-matched R and Bioconductor versions (R-3.3.1 should be running BioC 3.4, not Bioc 3.2), the fix is probably not to install devel versions of other packages.

Anyway, the error you are getting is from Hadley's readr package, which is not a Bioc package at all. You can always use read.table instead, or alternatively you could install the release version of readr, which is certainly working for me.