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Package 215/264HostnameOS / ArchBUILDCHECKBUILD BIN
rsbml 1.5.1
Michael Lawrence
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rsbml
Last Changed Rev: 30883 / Revision: 30951
Last Changed Date: 2008-04-07 09:57:56 -0700 (Mon, 07 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  ERROR  skipped 
wilson2 Linux (openSUSE 10.3) / x86_64  ERROR  skipped 
wellington Linux (openSUSE 10.3) / i686  ERROR  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ ERROR ] skipped  skipped 
pelham Mac OS X Leopard (10.5.1) / i386  ERROR  skipped  skipped 
Package: rsbml
Version: 1.5.1
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build rsbml
StartedAt: 2008-04-09 04:09:20 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 04:09:34 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 14.1 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'rsbml/DESCRIPTION' ... OK
* preparing 'rsbml':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst168472964


---------- Making package rsbml ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making StringMap.d from StringMap.c
making check.d from check.c
making doc.d from doc.c
making dom.d from dom.c
making graph.d from graph.c
making init.d from init.c
making io.d from io.c
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c StringMap.c -o StringMap.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/common.h:87,
                 from StringMap.c:52:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c check.c -o check.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLDocument.h:56,
                 from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLTypes.h:56,
                 from rsbml.h:4,
                 from check.c:1:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c doc.c -o doc.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLDocument.h:56,
                 from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLTypes.h:56,
                 from rsbml.h:4,
                 from doc.c:1:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c dom.c -o dom.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLDocument.h:56,
                 from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLTypes.h:56,
                 from rsbml.h:4,
                 from dom.c:1:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
dom.c: In function 'rsbml_build_dom_s_base':
dom.c:138: warning: implicit declaration of function 'SBase_getElementName'
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c graph.c -o graph.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLDocument.h:56,
                 from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLTypes.h:56,
                 from rsbml.h:4,
                 from graph.c:1:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c init.c -o init.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLDocument.h:56,
                 from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLTypes.h:56,
                 from rsbml.h:4,
                 from init.c:1:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include   -g -D_R_=1 -DUSE_R=1 -IC:/SBML/libsbml-2.3.4-expat/win32/include -IC:/SBML/libsbml-2.3.4-expat/win32/include/expat -Ie:/biocbld/bbs-2.2-bioc/R/include  -O3 -Wall  -c io.c -o io.o
In file included from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLDocument.h:56,
                 from C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/SBMLTypes.h:56,
                 from rsbml.h:4,
                 from io.c:1:
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:79: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:84: warning: ignoring #pragma warning 
C:/SBML/libsbml-2.3.4-expat/win32/include/sbml/common/extern.h:87: warning: ignoring #pragma warning 
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i rsbml_res.rc -o rsbml_res.o
gcc  -std=gnu99  -shared -s  -o rsbml.dll rsbml.def StringMap.o check.o doc.o dom.o graph.o init.o io.o rsbml_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin -LC:/SBML/libsbml-2.3.4-expat/win32/bin -lsbml   -lR
StringMap.o: In function `StringMapItem_create':
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/StringMap.c:101: undefined reference to `safe_malloc'
StringMap.o: In function `StringMap_create':
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/StringMap.c:83: undefined reference to `safe_malloc'
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/StringMap.c:84: undefined reference to `safe_calloc'
StringMap.o: In function `StringMap_grow':
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/StringMap.c:281: undefined reference to `safe_calloc'
StringMap.o: In function `StringMapItem_create':
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/StringMap.c:101: undefined reference to `safe_malloc'
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/StringMap.c:101: undefined reference to `safe_malloc'
dom.o: In function `rsbml_build_dom_s_base':
e:\biocbld\bbs-2.2-bioc\meat\rsbml\src/dom.c:138: undefined reference to `SBase_getElementName'
collect2: ld returned 1 exit status
make[3]: *** [rsbml.dll] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-rsbml] Error 2
*** Installation of rsbml failed ***

Removing 'E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst168472964/rsbml'
* creating vignettes ... ERROR

Error: processing vignette 'quick-start.Rnw' failed with diagnostics:
 chunk 1 (label=read) 
Error in library(rsbml) : there is no package called 'rsbml'
Execution halted