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Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/madman/Rpacks/adSplit.Rcheck'
* using Version 2.3.0 (2006-04-24)
* checking for file 'adSplit/DESCRIPTION' ... OK
* this is package 'adSplit' version '1.2.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'adSplit' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating adSplit-Ex.R ... OK
* checking examples ... ERROR
Running examples in adSplit-Ex.R failed.
The error most likely occurred in:

> ### * adSplit
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: adSplit
> ### Title: Annotation-Driven Splits
> ### Aliases: adSplit
> ### Keywords: datagen
> 
> ### ** Examples
>  
> # prepare data
> library(golubEsets) 
> data(Golub_Merge) 
> 
> # generate annotation-driven splits for apoptosis and signal transduction
> x <- adSplit(Golub_Merge, "GO:0006915", "hu6800")
Loading required package: hu6800
Evaluating identifier GO:0006915 with 537 probesets...
> x <- adSplit(Golub_Merge, c("GO:0007165","GO:0006915"), "hu6800", max.probes=7000)
Evaluating identifier GO:0007165 with 2516 probesets...
Evaluating identifier GO:0006915 with 537 probesets...
> 
> # generate a split for glutamate metabolism including 
> # an empirical p-value
> x <- adSplit(Golub_Merge, "KEGG:00251", "hu6800", B=100)
Evaluating identifier KEGG:00251 with 27 probesets...
> 
> # generate splits for all KEGG pathways.
> x <- adSplit(Golub_Merge, "KEGG", "hu6800")
Evaluating identifier KEGG:00010 with 66 probesets...
Evaluating identifier KEGG:00020 with 21 probesets...
Evaluating identifier KEGG:00030 with 21 probesets...
Evaluating identifier KEGG:00031 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00040 with 12 probesets...
 -> skipped, too few probes associated (12)
Evaluating identifier KEGG:00051 with 26 probesets...
Evaluating identifier KEGG:00052 with 27 probesets...
Evaluating identifier KEGG:00053 with 7 probesets...
 -> skipped, too few probes associated (7)
Evaluating identifier KEGG:00061 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00062 with 11 probesets...
 -> skipped, too few probes associated (11)
Evaluating identifier KEGG:00071 with 41 probesets...
Evaluating identifier KEGG:00072 with 7 probesets...
 -> skipped, too few probes associated (7)
Evaluating identifier KEGG:00100 with 13 probesets...
 -> skipped, too few probes associated (13)
Evaluating identifier KEGG:00120 with 31 probesets...
Evaluating identifier KEGG:00130 with 1 probesets...
 -> skipped, too few probes associated (1)
Evaluating identifier KEGG:00140 with 14 probesets...
 -> skipped, too few probes associated (14)
Evaluating identifier KEGG:00150 with 35 probesets...
Evaluating identifier KEGG:00190 with 66 probesets...
Evaluating identifier KEGG:00193 with 25 probesets...
Evaluating identifier KEGG:00220 with 23 probesets...
Evaluating identifier KEGG:00230 with 107 probesets...
Evaluating identifier KEGG:00240 with 52 probesets...
Evaluating identifier KEGG:00251 with 27 probesets...
Evaluating identifier KEGG:00252 with 24 probesets...
Evaluating identifier KEGG:00260 with 33 probesets...
Evaluating identifier KEGG:00271 with 10 probesets...
 -> skipped, too few probes associated (10)
Evaluating identifier KEGG:00272 with 12 probesets...
 -> skipped, too few probes associated (12)
Evaluating identifier KEGG:00280 with 48 probesets...
Evaluating identifier KEGG:00290 with 10 probesets...
 -> skipped, too few probes associated (10)
Evaluating identifier KEGG:00300 with 1 probesets...
 -> skipped, too few probes associated (1)
Evaluating identifier KEGG:00310 with 36 probesets...
Evaluating identifier KEGG:00330 with 52 probesets...
Evaluating identifier KEGG:00340 with 37 probesets...
Evaluating identifier KEGG:00350 with 50 probesets...
Evaluating identifier KEGG:00351 with 1 probesets...
 -> skipped, too few probes associated (1)
Evaluating identifier KEGG:00360 with 29 probesets...
Evaluating identifier KEGG:00361 with 17 probesets...
 -> skipped, too few probes associated (17)
Evaluating identifier KEGG:00362 with 5 probesets...
 -> skipped, too few probes associated (5)
Evaluating identifier KEGG:00363 with 4 probesets...
 -> skipped, too few probes associated (4)
Evaluating identifier KEGG:00380 with 49 probesets...
Evaluating identifier KEGG:00400 with 9 probesets...
 -> skipped, too few probes associated (9)
Evaluating identifier KEGG:00401 with 3 probesets...
 -> skipped, too few probes associated (3)
Evaluating identifier KEGG:00410 with 29 probesets...
Evaluating identifier KEGG:00430 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00440 with 7 probesets...
 -> skipped, too few probes associated (7)
Evaluating identifier KEGG:00450 with 15 probesets...
 -> skipped, too few probes associated (15)
Evaluating identifier KEGG:00460 with 7 probesets...
 -> skipped, too few probes associated (7)
Evaluating identifier KEGG:00471 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00472 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00480 with 27 probesets...
Evaluating identifier KEGG:00500 with 38 probesets...
Evaluating identifier KEGG:00510 with 24 probesets...
Evaluating identifier KEGG:00511 with 9 probesets...
 -> skipped, too few probes associated (9)
Evaluating identifier KEGG:00512 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00513 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00520 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00521 with 7 probesets...
 -> skipped, too few probes associated (7)
Evaluating identifier KEGG:00530 with 20 probesets...
Evaluating identifier KEGG:00531 with 15 probesets...
 -> skipped, too few probes associated (15)
Evaluating identifier KEGG:00533 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00534 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00550 with 1 probesets...
 -> skipped, too few probes associated (1)
Evaluating identifier KEGG:00561 with 43 probesets...
Evaluating identifier KEGG:00562 with 49 probesets...
Evaluating identifier KEGG:00563 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00564 with 39 probesets...
Evaluating identifier KEGG:00590 with 40 probesets...
Evaluating identifier KEGG:00591 with 22 probesets...
Evaluating identifier KEGG:00600 with 21 probesets...
Evaluating identifier KEGG:00601 with 9 probesets...
 -> skipped, too few probes associated (9)
Evaluating identifier KEGG:00602 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00603 with 11 probesets...
 -> skipped, too few probes associated (11)
Evaluating identifier KEGG:00604 with 6 probesets...
 -> skipped, too few probes associated (6)
Evaluating identifier KEGG:00620 with 36 probesets...
Evaluating identifier KEGG:00623 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00624 with 17 probesets...
 -> skipped, too few probes associated (17)
Evaluating identifier KEGG:00625 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00626 with 4 probesets...
 -> skipped, too few probes associated (4)
Evaluating identifier KEGG:00628 with 1 probesets...
 -> skipped, too few probes associated (1)
Evaluating identifier KEGG:00630 with 5 probesets...
 -> skipped, too few probes associated (5)
Evaluating identifier KEGG:00632 with 32 probesets...
Evaluating identifier KEGG:00640 with 28 probesets...
Evaluating identifier KEGG:00642 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00643 with 3 probesets...
 -> skipped, too few probes associated (3)
Evaluating identifier KEGG:00650 with 42 probesets...
Evaluating identifier KEGG:00660 with 1 probesets...
 -> skipped, too few probes associated (1)
Evaluating identifier KEGG:00670 with 16 probesets...
 -> skipped, too few probes associated (16)
Evaluating identifier KEGG:00680 with 13 probesets...
 -> skipped, too few probes associated (13)
Evaluating identifier KEGG:00710 with 23 probesets...
Evaluating identifier KEGG:00720 with 6 probesets...
 -> skipped, too few probes associated (6)
Evaluating identifier KEGG:00730 with 3 probesets...
 -> skipped, too few probes associated (3)
Evaluating identifier KEGG:00740 with 12 probesets...
 -> skipped, too few probes associated (12)
Evaluating identifier KEGG:00750 with 5 probesets...
 -> skipped, too few probes associated (5)
Evaluating identifier KEGG:00760 with 33 probesets...
Evaluating identifier KEGG:00770 with 11 probesets...
 -> skipped, too few probes associated (11)
Evaluating identifier KEGG:00780 with 3 probesets...
 -> skipped, too few probes associated (3)
Evaluating identifier KEGG:00790 with 19 probesets...
 -> skipped, too few probes associated (19)
Evaluating identifier KEGG:00791 with 3 probesets...
 -> skipped, too few probes associated (3)
Evaluating identifier KEGG:00830 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00860 with 24 probesets...
Evaluating identifier KEGG:00900 with 4 probesets...
 -> skipped, too few probes associated (4)
Evaluating identifier KEGG:00902 with 2 probesets...
 -> skipped, too few probes associated (2)
Evaluating identifier KEGG:00903 with 20 probesets...
Evaluating identifier KEGG:00910 with 17 probesets...
 -> skipped, too few probes associated (17)
Evaluating identifier KEGG:00920 with 7 probesets...
 -> skipped, too few probes associated (7)
Evaluating identifier KEGG:00930 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00940 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:00950 with 5 probesets...
 -> skipped, too few probes associated (5)
Evaluating identifier KEGG:00960 with 16 probesets...
 -> skipped, too few probes associated (16)
Evaluating identifier KEGG:00970 with 23 probesets...
Evaluating identifier KEGG:00980 with 52 probesets...
Evaluating identifier KEGG:01030 with 39 probesets...
Evaluating identifier KEGG:01031 with 30 probesets...
Evaluating identifier KEGG:01032 with 23 probesets...
Evaluating identifier KEGG:01430 with 124 probesets...
Evaluating identifier KEGG:01510 with 51 probesets...
Evaluating identifier KEGG:02010 with 24 probesets...
Evaluating identifier KEGG:03010 with 85 probesets...
Evaluating identifier KEGG:03020 with 12 probesets...
 -> skipped, too few probes associated (12)
Evaluating identifier KEGG:03022 with 28 probesets...
Evaluating identifier KEGG:03030 with 14 probesets...
 -> skipped, too few probes associated (14)
Evaluating identifier KEGG:03050 with 27 probesets...
Evaluating identifier KEGG:03060 with 8 probesets...
 -> skipped, too few probes associated (8)
Evaluating identifier KEGG:04010 with 263 probesets...
Evaluating identifier KEGG:04020 with 187 probesets...
Evaluating identifier KEGG:04060 with 243 probesets...
Evaluating identifier KEGG:04070 with 77 probesets...
Evaluating identifier KEGG:04080 with 259 probesets...
Evaluating identifier KEGG:04110 with 106 probesets...
Evaluating identifier KEGG:04120 with 23 probesets...
Evaluating identifier KEGG:04130 with 14 probesets...
 -> skipped, too few probes associated (14)
Evaluating identifier KEGG:04150 with 36 probesets...
Evaluating identifier KEGG:04210 with 94 probesets...
Evaluating identifier KEGG:04310 with 91 probesets...
Evaluating identifier KEGG:04320 with 28 probesets...
Evaluating identifier KEGG:04330 with 30 probesets...
Evaluating identifier KEGG:04340 with 30 probesets...
Evaluating identifier KEGG:04350 with 80 probesets...
Evaluating identifier KEGG:04360 with 91 probesets...
Evaluating identifier KEGG:04510 with 218 probesets...
Evaluating identifier KEGG:04512 with 101 probesets...
Evaluating identifier KEGG:04514 with 118 probesets...
Evaluating identifier KEGG:04520 with 73 probesets...
Evaluating identifier KEGG:04530 with 87 probesets...
Evaluating identifier KEGG:04540 with 99 probesets...
Evaluating identifier KEGG:04610 with 81 probesets...
Evaluating identifier KEGG:04612 with 105 probesets...
Evaluating identifier KEGG:04620 with 94 probesets...
Evaluating identifier KEGG:04630 with 141 probesets...
Evaluating identifier KEGG:04640 with 119 probesets...
Evaluating identifier KEGG:04650 with 131 probesets...
Evaluating identifier KEGG:04660 with 91 probesets...
Evaluating identifier KEGG:04662 with 67 probesets...
Evaluating identifier KEGG:04664 with 73 probesets...
Evaluating identifier KEGG:04670 with 105 probesets...
Evaluating identifier KEGG:04710 with 10 probesets...
 -> skipped, too few probes associated (10)
Evaluating identifier KEGG:04720 with 81 probesets...
Evaluating identifier KEGG:04730 with 81 probesets...
Evaluating identifier KEGG:04810 with 195 probesets...
Evaluating identifier KEGG:04910 with 123 probesets...
Evaluating identifier KEGG:04920 with 63 probesets...
Evaluating identifier KEGG:04930 with 47 probesets...
Evaluating identifier KEGG:04940 with 76 probesets...
Evaluating identifier KEGG:04950 with 24 probesets...
Evaluating identifier KEGG:05010 with 32 probesets...
Evaluating identifier KEGG:05020 with 12 probesets...
 -> skipped, too few probes associated (12)
Evaluating identifier KEGG:05030 with 19 probesets...
 -> skipped, too few probes associated (19)
Evaluating identifier KEGG:05040 with 45 probesets...
Evaluating identifier KEGG:05050 with 24 probesets...
Evaluating identifier KEGG:05060 with 12 probesets...
 -> skipped, too few probes associated (12)
Evaluating identifier KEGG:05110 with 26 probesets...
Evaluating identifier KEGG:05120 with 53 probesets...
> image(x)
Warning: unable to open connection to X11 display ''
Error in X11(display, width, height, pointsize, if (is.null(gamma)) 1 else gamma,  : 
	unable to start device X11
Execution halted