git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/multtest@48397 bc3139a8-67e5-0310-9ffc-ced21a209358
Katherine S. Pollard authored on 24/07/2010 21:55:59
| ... | ... |
@@ -281,6 +281,7 @@ EBMTP<-function(X,W=NULL,Y=NULL,Z=NULL,Z.incl=NULL,Z.test=NULL,na.rm=TRUE,test=" |
| 281 | 281 |
## Check installation of packages |
| 282 | 282 |
have_snow <- qRequire("snow")
|
| 283 | 283 |
if(!have_snow) stop("The package snow is required to use a cluster. Either snow is not installed or it is not in the standard library location.")
|
| 284 |
+ library("snow") #use library() since several functions are needed
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|
| 284 | 285 |
if (is.null(type)) |
| 285 | 286 |
stop("Must specify type argument to use a cluster. Alternatively, provide a cluster object as the argument to cluster.")
|
| 286 | 287 |
if (type=="SOCK") |
| ... | ... |
@@ -290,16 +291,19 @@ EBMTP<-function(X,W=NULL,Y=NULL,Z=NULL,Z.incl=NULL,Z.test=NULL,na.rm=TRUE,test=" |
| 290 | 291 |
else if (type=="MPI"){
|
| 291 | 292 |
have_rmpi <- qRequire("Rmpi")
|
| 292 | 293 |
if(!have_rmpi) stop("The package Rmpi is required for the specified type. Either Rmpi is not installed or it is not in the standard library location.")
|
| 293 |
- } |
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| 294 |
+ library("Rmpi")
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|
| 295 |
+ } |
|
| 294 | 296 |
else if (type=="PVM"){
|
| 295 | 297 |
have_rpvm <- qRequire("rpvm")
|
| 296 | 298 |
if(!have_rpvm) stop("The package rpvm is required for the specified type. Either rpvm is not installed or it is not in the standard library location.")
|
| 299 |
+ library("rpvm")
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|
| 297 | 300 |
} |
| 298 | 301 |
cluster <- makeCluster(cluster, type) |
| 299 | 302 |
clusterEvalQ(cluster, {library(Biobase); library(multtest)})
|
| 300 | 303 |
if (is.null(dispatch)) dispatch=0.05 |
| 301 | 304 |
} |
| 302 |
- } else if(inherits(cluster,c("MPIcluster", "PVMcluster", "SOCKcluster"))){
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|
| 305 |
+ } |
|
| 306 |
+ else if(inherits(cluster,c("MPIcluster", "PVMcluster", "SOCKcluster"))){
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|
| 303 | 307 |
clusterEvalQ(cluster, {library(Biobase); library(multtest)})
|
| 304 | 308 |
if (is.null(dispatch)) dispatch=0.05 |
| 305 | 309 |
} |
| ... | ... |
@@ -342,6 +342,7 @@ MTP<-function(X,W=NULL,Y=NULL,Z=NULL,Z.incl=NULL,Z.test=NULL,na.rm=TRUE,test="t. |
| 342 | 342 |
## Check installation of packages |
| 343 | 343 |
have_snow <- qRequire("snow")
|
| 344 | 344 |
if(!have_snow) stop("The package snow is required to use a cluster. Either snow is not installed or it is not in the standard library location.")
|
| 345 |
+ library("snow") #use library() since several functions are needed
|
|
| 345 | 346 |
if (is.null(type)) |
| 346 | 347 |
stop("Must specify type argument to use a cluster. Alternatively, provide a cluster object as the argument to cluster.")
|
| 347 | 348 |
if (type=="SOCK") |
| ... | ... |
@@ -351,16 +352,19 @@ MTP<-function(X,W=NULL,Y=NULL,Z=NULL,Z.incl=NULL,Z.test=NULL,na.rm=TRUE,test="t. |
| 351 | 352 |
else if (type=="MPI"){
|
| 352 | 353 |
have_rmpi <- qRequire("Rmpi")
|
| 353 | 354 |
if(!have_rmpi) stop("The package Rmpi is required for the specified type. Either Rmpi is not installed or it is not in the standard library location.")
|
| 355 |
+ library("Rmpi")
|
|
| 354 | 356 |
} |
| 355 | 357 |
else if (type=="PVM"){
|
| 356 | 358 |
have_rpvm <- qRequire("rpvm")
|
| 357 | 359 |
if(!have_rpvm) stop("The package rpvm is required for the specified type. Either rpvm is not installed or it is not in the standard library location.")
|
| 360 |
+ library("rpvm")
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|
| 358 | 361 |
} |
| 359 | 362 |
cluster <- makeCluster(cluster, type) |
| 360 | 363 |
clusterEvalQ(cluster, {library(Biobase); library(multtest)})
|
| 361 | 364 |
if (is.null(dispatch)) dispatch=0.05 |
| 362 | 365 |
} |
| 363 |
- } else if(inherits(cluster,c("MPIcluster", "PVMcluster", "SOCKcluster"))){
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|
| 366 |
+ } |
|
| 367 |
+ else if(inherits(cluster,c("MPIcluster", "PVMcluster", "SOCKcluster"))){
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|
| 364 | 368 |
clusterEvalQ(cluster, {library(Biobase); library(multtest)})
|
| 365 | 369 |
if (is.null(dispatch)) dispatch=0.05 |
| 366 | 370 |
} |