Package: RMAGEML

Version: 2.11.1

Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD build RMAGEML

RetCode: 1

Time: 2.5 seconds

Status: ERROR

PackageFile: None

* checking for file 'RMAGEML/DESCRIPTION' ... OK
* preparing 'RMAGEML':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
installing R.css in D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst749288522


---------- Making package RMAGEML ------------

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************

  adding build stamp to DESCRIPTION
  making DLL ...
making rmageml.d from rmageml.c
gcc  -IC:/progra~1/java/jdk1.5.0_01/include -IC:/progra~1/java/jdk1.5.0_01/include/win32 -Id:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c rmageml.c -o rmageml.o
rmageml.c:7:17: jni.h: No such file or directory
rmageml.c: In function `arji_createJVM':
rmageml.c:45: error: `JNIEnv' undeclared (first use in this function)
rmageml.c:45: error: (Each undeclared identifier is reported only once
rmageml.c:45: error: for each function it appears in.)
rmageml.c:45: error: `env' undeclared (first use in this function)
rmageml.c:46: error: `JavaVM' undeclared (first use in this function)
rmageml.c:46: error: `jvm' undeclared (first use in this function)
rmageml.c:47: error: `jint' undeclared (first use in this function)
rmageml.c:47: error: syntax error before "res"
rmageml.c:49: error: `JavaVMInitArgs' undeclared (first use in this function)
rmageml.c:49: error: syntax error before "vm_args"
rmageml.c:50: error: `JavaVMOption' undeclared (first use in this function)
rmageml.c:57: error: `options' undeclared (first use in this function)
rmageml.c:59: error: `vm_args' undeclared (first use in this function)
rmageml.c:62: error: `JNI_TRUE' undeclared (first use in this function)
rmageml.c:65: error: `res' undeclared (first use in this function)
rmageml.c:65: warning: implicit declaration of function `JNI_CreateJavaVM'
rmageml.c: In function `arji_destroyJavaVM':
rmageml.c:78: error: `JavaVM' undeclared (first use in this function)
rmageml.c:78: error: `thisjvm' undeclared (first use in this function)
rmageml.c:79: error: syntax error before ')' token
rmageml.c:80: error: syntax error before ')' token
rmageml.c: In function `destroyOM':
rmageml.c:86: error: `JNIEnv' undeclared (first use in this function)
rmageml.c:86: error: `env' undeclared (first use in this function)
rmageml.c:87: error: `jvm' undeclared (first use in this function)
rmageml.c:88: error: `jobject' undeclared (first use in this function)
rmageml.c:88: error: syntax error before "rmagestk"
rmageml.c:90: error: syntax error before ')' token
rmageml.c:91: error: syntax error before ')' token
rmageml.c:92: error: `JNI_VERSION_1_2' undeclared (first use in this function)
rmageml.c:93: error: `rmagestk' undeclared (first use in this function)
rmageml.c:93: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:95: warning: no return statement in function returning non-void
rmageml.c: In function `newRMAGESTK':
rmageml.c:100: error: `jclass' undeclared (first use in this function)
rmageml.c:100: error: syntax error before "cls"
rmageml.c:103: error: `jmethodID' undeclared (first use in this function)
rmageml.c:103: error: syntax error before "mid"
rmageml.c:104: error: `jstring' undeclared (first use in this function)
rmageml.c:107: error: syntax error before ')' token
rmageml.c:108: error: syntax error before ')' token
rmageml.c:112: error: `cls' undeclared (first use in this function)
rmageml.c:113: error: `mid' undeclared (first use in this function)
rmageml.c:114: error: `jstr' undeclared (first use in this function)
rmageml.c: In function `importFeatures':
rmageml.c:124: error: syntax error before "cls"
rmageml.c:132: error: syntax error before ')' token
rmageml.c:133: error: syntax error before ')' token
rmageml.c:136: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:140: error: `jpackage' undeclared (first use in this function)
rmageml.c:141: error: `jarrayID' undeclared (first use in this function)
rmageml.c:142: error: `jDED' undeclared (first use in this function)
rmageml.c:143: error: `jdb' undeclared (first use in this function)
rmageml.c: In function `getGridDimensions':
rmageml.c:157: error: syntax error before "cls"
rmageml.c:160: error: `jintArray' undeclared (first use in this function)
rmageml.c:163: error: `jint' undeclared (first use in this function)
rmageml.c:167: error: syntax error before ')' token
rmageml.c:168: error: syntax error before ')' token
rmageml.c:171: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:179: error: `result' undeclared (first use in this function)
rmageml.c:183: error: syntax error before "buf"
rmageml.c:185: error: `buf' undeclared (first use in this function)
rmageml.c:189: error: `i' undeclared (first use in this function)
rmageml.c: In function `selectQTypesDeriv':
rmageml.c:201: error: syntax error before "cls"
rmageml.c:209: error: syntax error before ')' token
rmageml.c:210: error: syntax error before ')' token
rmageml.c:213: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:216: error: `jQTD' undeclared (first use in this function)
rmageml.c:217: error: `jderiv' undeclared (first use in this function)
rmageml.c:220: error: syntax error before "buf"
rmageml.c: In function `getSizeDED':
rmageml.c:235: error: syntax error before "cls"
rmageml.c:243: error: syntax error before ')' token
rmageml.c:244: error: syntax error before ')' token
rmageml.c:247: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:266: error: syntax error before "buf"
rmageml.c: In function `selectQTypes':
rmageml.c:281: error: syntax error before "cls"
rmageml.c:293: error: syntax error before ')' token
rmageml.c:294: error: syntax error before ')' token
rmageml.c:297: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:303: error: `jrf' undeclared (first use in this function)
rmageml.c:304: error: `jrb' undeclared (first use in this function)
rmageml.c:305: error: `jgf' undeclared (first use in this function)
rmageml.c:306: error: `jgb' undeclared (first use in this function)
rmageml.c:316: error: syntax error before "buf"
rmageml.c: In function `getExternalData':
rmageml.c:335: error: syntax error before "cls"
rmageml.c:338: error: `jobjectArray' undeclared (first use in this function)
rmageml.c:342: error: `jsize' undeclared (first use in this function)
rmageml.c:347: error: syntax error before ')' token
rmageml.c:348: error: syntax error before ')' token
rmageml.c:351: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:363: error: `alen' undeclared (first use in this function)
rmageml.c:367: error: syntax error before "jstr"
rmageml.c: In function `getQuantitationTypes':
rmageml.c:382: error: syntax error before "cls"
rmageml.c:392: error: syntax error before ')' token
rmageml.c:393: error: syntax error before ')' token
rmageml.c:396: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:408: error: syntax error before "jstr"
rmageml.c: In function `getQTypeDescription':
rmageml.c:423: error: syntax error before "cls"
rmageml.c:430: error: syntax error before ')' token
rmageml.c:431: error: syntax error before ')' token
rmageml.c:434: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:437: error: `jQTypeID' undeclared (first use in this function)
rmageml.c: In function `createNewQTDim':
rmageml.c:457: error: syntax error before "cls"
rmageml.c:462: error: syntax error before ')' token
rmageml.c:463: error: syntax error before ')' token
rmageml.c:466: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:470: error: `jqtdimsize' undeclared (first use in this function)
rmageml.c:470: error: syntax error before "INTEGER"
rmageml.c: In function `addQuantitationTypeInfo':
rmageml.c:478: error: syntax error before "cls"
rmageml.c:488: error: syntax error before ')' token
rmageml.c:489: error: syntax error before ')' token
rmageml.c:492: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:496: error: `jqtID' undeclared (first use in this function)
rmageml.c:497: error: `jqtName' undeclared (first use in this function)
rmageml.c:498: error: `jqtDescription' undeclared (first use in this function)
rmageml.c:499: error: `jqtScale' undeclared (first use in this function)
rmageml.c:500: error: `jqtDataType' undeclared (first use in this function)
rmageml.c:501: error: `jderived' undeclared (first use in this function)
rmageml.c: In function `createNewMBASet':
rmageml.c:518: error: syntax error before "cls"
rmageml.c:523: error: syntax error before ')' token
rmageml.c:524: error: syntax error before ')' token
rmageml.c:527: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:531: error: `jsizeMBA' undeclared (first use in this function)
rmageml.c:531: error: syntax error before "INTEGER"
rmageml.c: In function `setMBA':
rmageml.c:542: error: syntax error before "cls"
rmageml.c:547: error: syntax error before ')' token
rmageml.c:548: error: syntax error before ')' token
rmageml.c:551: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:554: error: `jmba' undeclared (first use in this function)
rmageml.c: In function `updateMAGEML':
rmageml.c:563: error: syntax error before "cls"
rmageml.c:580: error: syntax error before ')' token
rmageml.c:581: error: syntax error before ')' token
rmageml.c:584: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:588: error: `jfile' undeclared (first use in this function)
rmageml.c:589: error: `jprotocolID' undeclared (first use in this function)
rmageml.c:590: error: `jprotocol' undeclared (first use in this function)
rmageml.c:591: error: `jdate' undeclared (first use in this function)
rmageml.c:592: error: `jqtDimID' undeclared (first use in this function)
rmageml.c:593: error: `jtransformationID' undeclared (first use in this function)
rmageml.c:596: error: `jBAD' undeclared (first use in this function)
rmageml.c:597: error: `jderivedBioAssayID' undeclared (first use in this function)
rmageml.c:598: error: `jderivedBioAssayDataID' undeclared (first use in this function)
rmageml.c:599: error: `jnumberOfFeatures' undeclared (first use in this function)
rmageml.c:599: error: syntax error before "INTEGER"
rmageml.c: In function `writeMAGEML':
rmageml.c:621: error: syntax error before "cls"
rmageml.c:627: error: syntax error before ')' token
rmageml.c:628: error: syntax error before ')' token
rmageml.c:631: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:635: error: `jdirectory' undeclared (first use in this function)
rmageml.c: In function `getVoidArrayInt':
rmageml.c:649: error: syntax error before "cls"
rmageml.c:657: error: syntax error before ')' token
rmageml.c:658: error: syntax error before ')' token
rmageml.c:661: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:666: error: syntax error before "buf"
rmageml.c: In function `getVoidArrayStr':
rmageml.c:684: error: syntax error before "cls"
rmageml.c:692: error: syntax error before ')' token
rmageml.c:693: error: syntax error before ')' token
rmageml.c:696: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:704: error: syntax error before "jstr"
rmageml.c: In function `getVoidStr':
rmageml.c:720: error: syntax error before "cls"
rmageml.c:726: error: syntax error before ')' token
rmageml.c:727: error: syntax error before ')' token
rmageml.c:730: error: syntax error before "R_ExternalPtrAddr"
rmageml.c: In function `getVoidVoid':
rmageml.c:745: error: syntax error before "cls"
rmageml.c:749: error: syntax error before ')' token
rmageml.c:750: error: syntax error before ')' token
rmageml.c:753: error: syntax error before "R_ExternalPtrAddr"
rmageml.c: At top level:
rmageml.c:17: warning: 'JavaMethod_type_tag' defined but not used
make[3]: *** [rmageml.o] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-RMAGEML] Error 2
*** Installation of RMAGEML failed ***

Removing 'D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst749288522/RMAGEML'
 ERROR
Installation failed.
Removing 'D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst749288522'