[BioC] about running gsva on mac

[Dan Tenenbaum]

On Thu, Aug 1, 2013 at 3:10 PM, Ed <edforum at gmail.com> wrote:
> Hi there,
>
> I used the examples in ?gsva and got the following errors on my mac.
> However, I run it also on the linux and it worked.
>
> Please suggest.
>
> Thanks,
>
> Weiwei
>
>> library(limma)
>>
>> p <- 10 ## number of genes
>> n <- 30 ## number of samples
>> nGrp1 <- 15 ## number of samples in group 1
>> nGrp2 <- n - nGrp1 ## number of samples in group 2
>>
>> ## consider three disjoint gene sets
>> geneSets <- list(set1=paste("g", 1:3, sep=""),
> +                  set2=paste("g", 4:6, sep=""),
> +                  set3=paste("g", 7:10, sep=""))
>>
>> ## sample data from a normal distribution with mean 0 and st.dev. 1
>> y <- matrix(rnorm(n*p), nrow=p, ncol=n,
> +             dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n,
> sep="")))
>>
>> ## genes in set1 are expressed at higher levels in the last 10 samples
>> y[geneSets$set1, (nGrp1+1):n] <- y[geneSets$set1, (nGrp1+1):n] + 2
>>
>> ## build design matrix
>> design <- cbind(sampleGroup1=1, sampleGroup2vs1=c(rep(0, nGrp1), rep(1,
> nGrp2)))
>>
>> ## fit linear model
>> fit <- lmFit(y, design)
>>
>> ## estimate moderated t-statistics
>> fit <- eBayes(fit)
>>
>> ## genes in set1 are differentially expressed
>> topTable(fit, coef="sampleGroup2vs1")
>     ID       logFC           t      P.Value    adj.P.Val         B
> 2   g2  2.43865785  6.79741169 1.490585e-09 1.490585e-08 11.467181
> 1   g1  1.81349993  5.04733755 2.590932e-06 1.295466e-05  4.218446
> 3   g3  1.68971708  4.54930258 1.812937e-05 6.043122e-05  2.348424
> 5   g5  0.25263973  0.65201092 5.161890e-01 9.308575e-01 -6.688660
> 10 g10  0.16766254  0.49082930 6.248376e-01 9.308575e-01 -6.780571
> 9   g9  0.13478444  0.40143265 6.891295e-01 9.308575e-01 -6.820434
> 8   g8 -0.12067327 -0.32614302 7.451340e-01 9.308575e-01 -6.847833
> 7   g7 -0.08002351 -0.23401984 8.155437e-01 9.308575e-01 -6.873660
> 4   g4  0.07875803  0.20538583 8.377717e-01 9.308575e-01 -6.879960
> 6   g6 -0.03196719 -0.08251146 9.344379e-01 9.344379e-01 -6.897676
>>
>> ## estimate GSVA enrichment scores for the three sets
>> gsva_es <- gsva(y, geneSets, mx.diff=1)$es.obs
>   |
>               |   0%The process has forked and you cannot use this
> CoreFoundation functionality safely. You MUST exec().
> Break on
> __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__()
> to debug.
> The process has forked and you can
>
>
>
>> version
>                _
> platform       x86_64-apple-darwin10.8.0
> arch           x86_64
> os             darwin10.8.0
> system         x86_64, darwin10.8.0
> status
> major          3
> minor          0.1
> year           2013
> month          05
> day            16
> svn rev        62743
> language       R
> version.string R version 3.0.1 (2013-05-16)
> nickname       Good Sport
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] limma_3.16.7         GSVA_1.8.0           GSEABase_1.22.0
>  graph_1.38.3
> [5] annotate_1.38.0      AnnotationDbi_1.22.6 Biobase_2.20.1
> BiocGenerics_0.6.0
> [9] BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
>  [1] DBI_0.2-7       grid_3.0.1      IRanges_1.18.2  lattice_0.20-15
> Matrix_1.0-12
>  [6] RSQLite_0.11.4  stats4_3.0.1    tools_3.0.1     XML_3.95-0.2
>  xtable_1.7-1
>>
>

I can't reproduce this on a Mac with similar sessionInfo. The
differences in sessionInfo() suggest things to try:

update the XML package:
library(BiocInstaller)
biocLite("XML")

Locale is also different so that would be another thing to explore if
these don't work.

Also, you have packages loaded that I do not have loaded. So try
starting R as follows:

R --vanilla

Here is my sessionInfo():

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

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

other attached packages:
[1] limma_3.16.7         GSVA_1.8.0           GSEABase_1.22.0
[4] graph_1.38.3         annotate_1.38.0      AnnotationDbi_1.22.6
[7] Biobase_2.20.1       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] DBI_0.2-7      IRanges_1.18.2 RSQLite_0.11.4 XML_3.98-1.1   stats4_3.0.1
[6] tools_3.0.1    xtable_1.7-1


Dan


>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor