- GlmEstimates (and the C code in wald test) is known to be quite buggy.
- test.allele.switch and mvtests mis-behave for sex chromosomes.
- imputation gives different outcomes on 32-bit vs 64-bit platforms (affects imputation vignette).
- ld calculation gives different outcomes on 32-bit vs 64-bit platforms (affects ld vignette).
- PCA calculation changes signs between R 2.15, R 3.0 and back in R 3.2 (affects PCA vignette).
- summary MAF gives different outcomes on 32-bit vs 64-bit platforms (affects snpStats vignette).
- 2-df single snp tests gives different outcomes on 32-bit vs 64-bit platforms (affects snpStats vignette).
- Form xobjects between 2.15 and R 3.0 (affects snpStats vignette)
* Not bugs:
changes r11513-r11516 in the survival package broke Family-practical8.
(problem in the survival package)
non-English graphics usage in offcial windows/Mac OS X builds of R.
(problem in bundled statically-linked outdated freetype)
"Found non-API call to R: ‘R_data_class’" appears in R 3.0.x/3.1.x checks.
(disappeared in R 3.2).
R 3.x is slower.
(problem in R)
Repeated runs of data-input-vignette.pdf, differences.pdf, Fst-vignette.pdf
differs by /CreationDate, /ModDate, /ID .
Repeated runs of imputation-vignette.pdf, ld-vignette.pdf,
pca-vignette.pdf, snpStats-vignette.pdf, tdt-vignette.pdf
differs by /CreationDate, /ModDate, /ID, and
embedded graphics' /CreationDate, /ModDate, /Producer(R ).