Hi Steve,

thank you for your help.

But I still face this problem even after I reinstalled R (version 2.15.0)
 and reinstalled all packages I need to devel versions .

With other packages I am using, for example: cummerbund 1.99.2, under devel
version
, everything is working fine.

I tested also all thing on windows, everything is working under devel
versions.

Is it a bug for Mac 10.7.4 ?

Regards,
Sheng

sessionInfo()

R version 2.15.0 (2012-03-30)

Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)


locale:

[1] C


attached base packages:

[1] grid      stats     graphics  grDevices utils     datasets  methods

[8] base


other attached packages:

 [1] cummeRbund_1.99.2                   fastcluster_1.1.6

 [3] reshape2_1.2.1                      ggplot2_0.9.1

 [5] RSQLite_0.11.1                      DBI_0.2-5

 [7] AnnotationDbi_1.19.9                BSgenome.Ecoli.NCBI.20080805_1.3.17

 [9] BSgenome_1.25.1                     GenomicRanges_1.9.21

[11] Biostrings_2.25.4                   IRanges_1.15.11

[13] multtest_2.13.0                     Biobase_2.17.5

[15] biomaRt_2.13.1                      BiocGenerics_0.3.0

[17] gplots_2.10.1                       KernSmooth_2.23-7

[19] caTools_1.13                        bitops_1.0-4.1

[21] gdata_2.8.2                         gtools_2.6.2

[23] BiocInstaller_1.5.10


loaded via a namespace (and not attached):

 [1] MASS_7.3-18        RColorBrewer_1.0-5 RCurl_1.91-1       XML_3.9-4


 [5] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2       labeling_0.1


 [9] memoise_0.1        munsell_0.3        plyr_1.7.1
proto_0.3-9.2

[13] scales_0.2.1       splines_2.15.0     stats4_2.15.0      stringr_0.6


[17] survival_2.36-14   tools_2.15.0

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