[Bioc-devel] edgeR crashes when xlsxjars is loaded

By the way, here is my sessionInfo after a successful run of the bug 
script (without loading xlsxjars):

sessionInfo()

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] locfit_1.5-9.1       edgeR_3.4.2          limma_3.18.5
 [4] foreach_1.4.1        plyr_1.8             stringr_0.6.2
 [7] IRanges_1.20.6       BiocGenerics_0.8.0   ggplot2_0.9.3.1
[10] BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] codetools_0.2-8    colorspace_1.2-4   dichromat_2.0-0    
digest_0.6.4
 [5] grid_3.0.2         gtable_0.1.2       iterators_1.0.6    
labeling_0.2
 [9] lattice_0.20-25    MASS_7.3-29        munsell_0.4.2      
proto_0.3-10
[13] RColorBrewer_1.0-5 reshape2_1.2.2     scales_0.2.3       
stats4_3.0.2

On Dec 16, 2013, at 5:20 PM, Ryan <rct at thompsonclan.org> wrote:

On Mon Dec 16 14:18:41 2013, Steve Lianoglou wrote:

On Mon, Dec 16, 2013 at 2:03 PM, Ryan <rct at thompsonclan.org> wrote:

I'm quite sure that it is an interaction between something that xlsxjars
does and edgeR's C code. The example I gave is a reduction from my actual
script, and I finally figured out that loading the xlsxjars package is what
triggers the crash. If I comment out the line that loads xlsxjars, then
everything runs just fine for me.

My current solution is to use the parallel package to load and use the xlsx
package only in subprocesses, so the main R process never uses java.

Out of curiosity, are you saying that if you simply load rJava instead
of xlsxjars in the same place (or perhaps load another package that
depends on rJava), is the crash avoided, too?

Yes, that's right, if I load rJava instead of xlsxjars, there is no crash. Perhaps loading rJava does not actually launch a Java subprocess, but loading xlxsjars does?

JVM is not started until you call

.jinit()

so try that ..