Odd characters in html report

[andrew-slater]

There seems to be some environment issue (only some users experience) where knitr2html gives different results for different users. When I run the example, report-short.html matches the expected output but when others run (Dana and possibly Li Li), the md files are identical (per diff) but in the html, the lambda symbol is replaced and there is something else in the Table 3 heading:

diff expected_report-short.html odd_report-short.html
469c469
<  

---
> <e2><80><83>
598c598
< for study arm.  ** The genomic control coefficient λ, estimated from

---
> for study arm.  ** The genomic control coefficient <ce><bb>, estimated from
602c602
< λ=1), and any residual test statistic inflation was corrected using

---
> <ce><bb>=1), and any residual test statistic inflation was corrected using

The examples are attached (had to add .txt extension to get to upload):
expected_report-short.html.txt
odd_report-short.html.txt

I think I confirmed with Dana that we are using the same instance of knitr but perhaps some different behavior when running through SGE.

/GWD/appbase/projects/statgen/GXapp/R3.0.0/R-3.0.0/bin/R
> requireNamespace("knitr")
Loading required namespace: knitr
> packageVersion("knitr")
[1] ‘1.6’
packinfo <- installed.packages(fields = c("Package", "LibPath"))
> packinfo["knitr",c("Package", "LibPath")]
                                               Package
                                               "knitr"
                                               LibPath
"/GWD/appbase/projects/statgen/R3.0.0/R-3.0.0/library"

When Angela ran the example, report-short.html also matched the expected output so she might be another tester.