DECIPHER 1.0.0
Erik Wright
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/DECIPHER | | Last Changed Rev: 59920 / Revision: 61898 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ ERROR ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ERROR | skipped | skipped |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/DECIPHER.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '1.0.0'
* 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 'DECIPHER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... NOTE
CreateChimeras: no visible binding for global variable 's1'
CreateChimeras: no visible binding for global variable 'd'
CreateChimeras: no visible binding for global variable 'myName'
* 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 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 examples ... ERROR
Running examples in 'DECIPHER-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Add2DB
> ### Title: Add Data To A Database
> ### Aliases: Add2DB
>
> ### ** Examples
>
> # Create a sequence database
> gen <- system.file("extdata", "Bacteria_175seqs.gen", package="DECIPHER")
> dbConn <- dbConnect(SQLite(), ":memory:")
> Seqs2DB(gen, "GenBank", dbConn, "Bacteria")
Reading GenBank file from line 0 to 99999
175 total sequences in database.
Time difference of 0.5 secs
[1] 175
>
> # Identify the sequence lengths
> l <- IdLengths(dbConn)
Lengths counted for 175 sequences.
>
> # Add lengths to the database
> Add2DB(l, dbConn)
Expression: alter table DNA add column bases INTEGER
Expression: update or replace DNA set bases = :bases where row_names = :row_names
Expression: alter table DNA add column nonbases INTEGER
Expression: update or replace DNA set nonbases = :nonbases where row_names = :row_names
Expression: alter table DNA add column width INTEGER
Expression: update or replace DNA set width = :width where row_names = :row_names
Added to table DNA: "bases" and "nonbases" and "width".
Time difference of 0 secs
[1] TRUE
>
> # View the added lengths
> BrowseDB(dbConn)
Error in shell.exec(url) :
problem in displaying 'E:\biocbld\bbs-2.9-bioc\tmpdir\RtmpMZzj0B/db.html'
Calls: BrowseDB -> browseURL -> shell.exec
Execution halted
* installing *source* package 'DECIPHER' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263:0: warning: ignoring #pragma omp parallel
ClusterNJ.c:273:0: warning: ignoring #pragma omp critical
ClusterNJ.c:433:0: warning: ignoring #pragma omp parallel
ClusterNJ.c:445:0: warning: ignoring #pragma omp parallel
ClusterNJ.c:193:18: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:194:16: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:195:12: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:195:29: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:192:56: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:192:62: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:506:19: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:590:19: warning: 'longestLeaf' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180:0: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:190:0: warning: ignoring #pragma omp critical
ClusterUPGMA.c:340:0: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:352:0: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:122:18: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:123:16: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:124:12: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:124:29: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:121:56: warning: 'minR' may be used uninitialized in this function
ClusterUPGMA.c:121:62: warning: 'minC' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171:0: warning: ignoring #pragma omp parallel
DistanceMatrix.c:131:25: warning: 'rPercentComplete' may be used uninitialized in this function
DistanceMatrix.c:133:12: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:133:29: warning: 'utilsPackage' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.9-bioc/R/library/stats/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def Biostrings_stubs.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'DECIPHERing.Rnw'
'FindChimeras.Rnw'
** testing if installed package can be loaded
* DONE (DECIPHER)