Run runQTLseqAnalysis subscript out of bounds

[trenk-nicolas]

I am following the Yang2013data tutorial and when running
df_filt <- runQTLseqAnalysis(df_filt, windowSize = 1e6, popStruc = "F2", bulkSize = c(385, 430), replications = 10000, intervals = c(95, 99) )

I get the warning:
Counting SNPs in each window...
Calculating tricube smoothed delta SNP index...
Returning the following two sided confidence intervals: 95, 99
Variable 'depth' not defined, using min and max depth from data: 40-197
Assuming bulks selected from F2 population, with 385 and 430 individuals per bulk.
Simulating 10000 SNPs with reads at each depth: 40-197
Keeping SNPs with >= 0.3 SNP-index in both simulated bulks
Joining with by = join_by(tricubeDP, CI_95, CI_99)
Warning message:
There were 5398 warnings in dplyr::mutate().
The first warning was:
ℹ In argument: nSNPs = countSNPs_cpp(POS = POS, windowSize = windowSize).
ℹ In group 1: CHROM = Chr1.
Caused by warning in countSNPs_cpp():
! subscript out of bounds (index 67784 >= vector size 67784)
ℹ Run dplyr::last_dplyr_warnings() to see the 5397 remaining warnings.

---

Backtrace:
▆

1. ├─QTLseqr::runQTLseqAnalysis(...)
2. │ └─SNPset %>% dplyr::group_by(CHROM) %>% ...
3. ├─dplyr::mutate(., nSNPs = countSNPs_cpp(POS = POS, windowSize = windowSize))
4. └─dplyr:::mutate.data.frame(...)

... with 5393 more warnings.
ℹ Run dplyr::last_dplyr_warnings(n = 10) to show more.

Is this anything that could cause problems?

[bmansfeld]

Hi I'm not sure what could be causing that.
Do you have a fresh installation of R and Rstudio? Rtools?