ddgraph 1.0.3
Robert Stojnic
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ddgraph | | Last Changed Rev: 66797 / Revision: 66885 | | Last Changed Date: 2012-06-18 07:40:12 -0700 (Mon, 18 Jun 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ddgraph.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ddgraph/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ddgraph' version '1.0.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'ddgraph' can be installed ... OK
* checking installed package size ... 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'ddgraph-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calcDependence
> ### Title: Dependence with target variable
> ### Aliases: calcDependence
>
> ### ** Examples
> # load in the data for fly mesoderm
> data(mesoBin)
>
> # increase alpha to 0.1, suppress progress output
> calcDependence(mesoBin$VM, "ncpc", alpha=0.05)
$obj
DDGraph produced with ncpc algorithm
Direct:
Joint: Bin 6-8h Bin 8-10h
Indirect: Tin 6-8h Bin 10-12h Twi 2-4h Twi 4-6h Bap 6-8h
Using P-value alpha cutoff = 0.05 with conditional independence test = "mc-x2-c"
$nbr
[1] "Bin 6-8h" "Bin 8-10h"
$labels
$labels$direct
NULL
$labels$joint
[1] "Bin 6-8h" "Bin 8-10h"
$labels$indirect
[1] "Tin 6-8h" "Bin 10-12h" "Twi 2-4h" "Twi 4-6h" "Bap 6-8h"
$table
name type explained.by explained.pval marginal.pval
5 Bin 8-10h joint Bin 6-8h 0.0614 0.0004
4 Bin 6-8h joint Bin 8-10h 0.0810 0.0006
10 Bap 6-8h weak indirect Bin 6-8h 0.0580 0.0058
6 Bin 10-12h weak indirect Bin 8-10h 1.0000 0.0138
7 Twi 2-4h weak indirect Bin 6-8h 0.1504 0.0216
8 Twi 4-6h weak indirect Bin 8-10h 0.1412 0.0268
3 Tin 6-8h weak indirect Bin 6-8h 0.6406 0.0318
2 Tin 4-6h no dependence NA 0.3974
9 Twi 6-8h no dependence NA 0.4272
15 Mef2 10-12h no dependence NA 0.4934
13 Mef2 6-8h no dependence NA 0.5844
12 Mef2 4-6h no dependence NA 0.5906
14 Mef2 8-10h no dependence NA 0.7392
1 Tin 2-4h no dependence NA 1.0000
11 Mef2 2-4h no dependence NA 1.0000
log2FC
5 2.6147098
4 1.9517448
10 1.6147098
6 1.8211607
7 -1.7776076
8 -2.4441838
3 1.1243842
2 0.4627068
9 -0.6416299
15 -1.2921808
13 -0.5729172
12 -0.4002405
14 -0.5816874
1 0.1996723
11 -0.5007674
>
> # run ncpc* with mutual information with shrinkage and minimal numbers of
> # samples per conditioning set of 15
> calcDependence(mesoBin$VM, "ncpc*", test.type="mi-sh", min.table.size=15)
$obj
DDGraph produced with ncpc* algorithm
Direct:
Joint: Bin 6-8h Bin 8-10h
Conditional:
Conditional joint:
Indirect: Tin 6-8h Bin 10-12h Twi 2-4h Twi 4-6h Bap 6-8h
Using P-value alpha cutoff = 0.05 with conditional independence test = "mi-sh"
$nbr
[1] "Bin 6-8h" "Bin 8-10h"
$mb
[1] "Bin 6-8h" "Bin 8-10h"
$labels
$labels$direct
NULL
$labels$joint
[1] "Bin 6-8h" "Bin 8-10h"
$labels$indirect
[1] "Tin 6-8h" "Bin 10-12h" "Twi 2-4h" "Twi 4-6h" "Bap 6-8h"
$labels$conditional
NULL
$labels$conditionalJoint
NULL
$table
name type explained.by explained.pval conditional.type
5 Bin 8-10h joint Bin 6-8h 0.1129735
4 Bin 6-8h joint Bin 8-10h 0.1543618
10 Bap 6-8h weak indirect Bin 6-8h 0.1077358
6 Bin 10-12h weak indirect Bin 8-10h 0.8052702
7 Twi 2-4h weak indirect Bin 6-8h 0.1527278
8 Twi 4-6h weak indirect Bin 8-10h 0.1125118
3 Tin 6-8h weak indirect Bin 6-8h 0.6210417
15 Mef2 10-12h no dependence NA
2 Tin 4-6h no dependence NA
9 Twi 6-8h no dependence NA
13 Mef2 6-8h no dependence NA
12 Mef2 4-6h no dependence NA
14 Mef2 8-10h no dependence NA
1 Tin 2-4h no dependence NA
11 Mef2 2-4h no dependence NA
conditional.on conditional.explained conditional.pval marginal.pval
5 0.0004145264
4 0.0005420886
10 0.0055307127
6 0.0135478039
7 0.0165514158
8 0.0172271300
3 0.0345167513
15 0.3338481472
2 0.3520964001
9 0.4145694525
13 0.4794555793
12 0.5676072714
14 0.5885109046
1 0.7031989752
11 0.7769814858
log2FC
5 2.6147098
4 1.9517448
10 1.6147098
6 1.8211607
7 -1.7776076
8 -2.4441838
3 1.1243842
15 -1.2921808
2 0.4627068
9 -0.6416299
13 -0.5729172
12 -0.4002405
14 -0.5816874
1 0.1996723
11 -0.5007674
>
> # run PC algorithm using the G^2 test from pcalg package
> calcDependence(mesoBin$VM, "pc", indepTest=pcalg::binCItest)
Error in lapply(X = X, FUN = FUN, ...) :
could not find function "strongComp"
Calls: calcDependence ... orderEdges -> stopifnot -> isAcyclic -> sapply -> lapply
Execution halted
* installing *source* package 'ddgraph' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -fPIC -g -O2 -Wall -fasm-blocks -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp: In function 'SEXPREC* mcX2CLoopC(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
mcX2cloop.cpp:14: warning: label 'Rcpp' defined but not used
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ddgraph.so mcX2cloop.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/ddgraph.Rcheck/ddgraph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'ddgraph'
** help
*** installing help indices
** building package indices
** installing vignettes
'ddgraph.Rnw'
** testing if installed package can be loaded
* DONE (ddgraph)