Package: RMAGEML

Version: 2.11.0

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/Rinst481259649


---------- 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:53: error: `options' undeclared (first use in this function)
rmageml.c:55: error: `vm_args' undeclared (first use in this function)
rmageml.c:58: error: `JNI_TRUE' undeclared (first use in this function)
rmageml.c:61: error: `res' undeclared (first use in this function)
rmageml.c:61: warning: implicit declaration of function `JNI_CreateJavaVM'
rmageml.c: In function `arji_destroyJavaVM':
rmageml.c:74: error: `JavaVM' undeclared (first use in this function)
rmageml.c:74: error: `thisjvm' undeclared (first use in this function)
rmageml.c:75: error: syntax error before ')' token
rmageml.c:76: error: syntax error before ')' token
rmageml.c: In function `destroyOM':
rmageml.c:82: error: `JNIEnv' undeclared (first use in this function)
rmageml.c:82: error: `env' undeclared (first use in this function)
rmageml.c:83: error: `jvm' undeclared (first use in this function)
rmageml.c:84: error: `jobject' undeclared (first use in this function)
rmageml.c:84: error: syntax error before "rmagestk"
rmageml.c:86: error: syntax error before ')' token
rmageml.c:87: error: syntax error before ')' token
rmageml.c:88: error: `JNI_VERSION_1_2' undeclared (first use in this function)
rmageml.c:89: error: `rmagestk' undeclared (first use in this function)
rmageml.c:89: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:91: warning: no return statement in function returning non-void
rmageml.c: In function `newRMAGESTK':
rmageml.c:96: error: `jclass' undeclared (first use in this function)
rmageml.c:96: error: syntax error before "cls"
rmageml.c:99: error: `jmethodID' undeclared (first use in this function)
rmageml.c:99: error: syntax error before "mid"
rmageml.c:100: error: `jstring' undeclared (first use in this function)
rmageml.c:103: error: syntax error before ')' token
rmageml.c:104: error: syntax error before ')' token
rmageml.c:108: error: `cls' undeclared (first use in this function)
rmageml.c:109: error: `mid' undeclared (first use in this function)
rmageml.c:110: error: `jstr' undeclared (first use in this function)
rmageml.c: In function `importFeatures':
rmageml.c:120: error: syntax error before "cls"
rmageml.c:128: error: syntax error before ')' token
rmageml.c:129: error: syntax error before ')' token
rmageml.c:132: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:136: error: `jpackage' undeclared (first use in this function)
rmageml.c:137: error: `jarrayID' undeclared (first use in this function)
rmageml.c:138: error: `jDED' undeclared (first use in this function)
rmageml.c:139: error: `jdb' undeclared (first use in this function)
rmageml.c: In function `getGridDimensions':
rmageml.c:153: error: syntax error before "cls"
rmageml.c:156: error: `jintArray' undeclared (first use in this function)
rmageml.c:159: error: `jint' undeclared (first use in this function)
rmageml.c:163: error: syntax error before ')' token
rmageml.c:164: error: syntax error before ')' token
rmageml.c:167: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:175: error: `result' undeclared (first use in this function)
rmageml.c:179: error: syntax error before "buf"
rmageml.c:181: error: `buf' undeclared (first use in this function)
rmageml.c:185: error: `i' undeclared (first use in this function)
rmageml.c: In function `selectQTypesDeriv':
rmageml.c:197: error: syntax error before "cls"
rmageml.c:205: error: syntax error before ')' token
rmageml.c:206: error: syntax error before ')' token
rmageml.c:209: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:212: error: `jQTD' undeclared (first use in this function)
rmageml.c:213: error: `jderiv' undeclared (first use in this function)
rmageml.c:216: error: syntax error before "buf"
rmageml.c: In function `getSizeDED':
rmageml.c:231: error: syntax error before "cls"
rmageml.c:239: error: syntax error before ')' token
rmageml.c:240: error: syntax error before ')' token
rmageml.c:243: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:262: error: syntax error before "buf"
rmageml.c: In function `selectQTypes':
rmageml.c:277: error: syntax error before "cls"
rmageml.c:289: error: syntax error before ')' token
rmageml.c:290: error: syntax error before ')' token
rmageml.c:293: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:299: error: `jrf' undeclared (first use in this function)
rmageml.c:300: error: `jrb' undeclared (first use in this function)
rmageml.c:301: error: `jgf' undeclared (first use in this function)
rmageml.c:302: error: `jgb' undeclared (first use in this function)
rmageml.c:312: error: syntax error before "buf"
rmageml.c: In function `getExternalData':
rmageml.c:331: error: syntax error before "cls"
rmageml.c:334: error: `jobjectArray' undeclared (first use in this function)
rmageml.c:338: error: `jsize' undeclared (first use in this function)
rmageml.c:343: error: syntax error before ')' token
rmageml.c:344: error: syntax error before ')' token
rmageml.c:347: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:359: error: `alen' undeclared (first use in this function)
rmageml.c:363: error: syntax error before "jstr"
rmageml.c: In function `getQuantitationTypes':
rmageml.c:378: error: syntax error before "cls"
rmageml.c:388: error: syntax error before ')' token
rmageml.c:389: error: syntax error before ')' token
rmageml.c:392: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:404: error: syntax error before "jstr"
rmageml.c: In function `getQTypeDescription':
rmageml.c:419: error: syntax error before "cls"
rmageml.c:426: error: syntax error before ')' token
rmageml.c:427: error: syntax error before ')' token
rmageml.c:430: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:433: error: `jQTypeID' undeclared (first use in this function)
rmageml.c: In function `createNewQTDim':
rmageml.c:453: error: syntax error before "cls"
rmageml.c:458: error: syntax error before ')' token
rmageml.c:459: error: syntax error before ')' token
rmageml.c:462: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:466: error: `jqtdimsize' undeclared (first use in this function)
rmageml.c:466: error: syntax error before "INTEGER"
rmageml.c: In function `addQuantitationTypeInfo':
rmageml.c:474: error: syntax error before "cls"
rmageml.c:484: error: syntax error before ')' token
rmageml.c:485: error: syntax error before ')' token
rmageml.c:488: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:492: error: `jqtID' undeclared (first use in this function)
rmageml.c:493: error: `jqtName' undeclared (first use in this function)
rmageml.c:494: error: `jqtDescription' undeclared (first use in this function)
rmageml.c:495: error: `jqtScale' undeclared (first use in this function)
rmageml.c:496: error: `jqtDataType' undeclared (first use in this function)
rmageml.c:497: error: `jderived' undeclared (first use in this function)
rmageml.c: In function `createNewMBASet':
rmageml.c:514: error: syntax error before "cls"
rmageml.c:519: error: syntax error before ')' token
rmageml.c:520: error: syntax error before ')' token
rmageml.c:523: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:527: error: `jsizeMBA' undeclared (first use in this function)
rmageml.c:527: error: syntax error before "INTEGER"
rmageml.c: In function `setMBA':
rmageml.c:538: error: syntax error before "cls"
rmageml.c:543: error: syntax error before ')' token
rmageml.c:544: error: syntax error before ')' token
rmageml.c:547: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:550: error: `jmba' undeclared (first use in this function)
rmageml.c: In function `updateMAGEML':
rmageml.c:559: error: syntax error before "cls"
rmageml.c:576: error: syntax error before ')' token
rmageml.c:577: error: syntax error before ')' token
rmageml.c:580: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:584: error: `jfile' undeclared (first use in this function)
rmageml.c:585: error: `jprotocolID' undeclared (first use in this function)
rmageml.c:586: error: `jprotocol' undeclared (first use in this function)
rmageml.c:587: error: `jdate' undeclared (first use in this function)
rmageml.c:588: error: `jqtDimID' undeclared (first use in this function)
rmageml.c:589: error: `jtransformationID' undeclared (first use in this function)
rmageml.c:592: error: `jBAD' undeclared (first use in this function)
rmageml.c:593: error: `jderivedBioAssayID' undeclared (first use in this function)
rmageml.c:594: error: `jderivedBioAssayDataID' undeclared (first use in this function)
rmageml.c:595: error: `jnumberOfFeatures' undeclared (first use in this function)
rmageml.c:595: error: syntax error before "INTEGER"
rmageml.c: In function `writeMAGEML':
rmageml.c:617: error: syntax error before "cls"
rmageml.c:623: error: syntax error before ')' token
rmageml.c:624: error: syntax error before ')' token
rmageml.c:627: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:631: error: `jdirectory' undeclared (first use in this function)
rmageml.c: In function `getVoidArrayInt':
rmageml.c:645: error: syntax error before "cls"
rmageml.c:653: error: syntax error before ')' token
rmageml.c:654: error: syntax error before ')' token
rmageml.c:657: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:662: error: syntax error before "buf"
rmageml.c: In function `getVoidArrayStr':
rmageml.c:680: error: syntax error before "cls"
rmageml.c:688: error: syntax error before ')' token
rmageml.c:689: error: syntax error before ')' token
rmageml.c:692: error: syntax error before "R_ExternalPtrAddr"
rmageml.c:700: error: syntax error before "jstr"
rmageml.c: In function `getVoidStr':
rmageml.c:716: error: syntax error before "cls"
rmageml.c:722: error: syntax error before ')' token
rmageml.c:723: error: syntax error before ')' token
rmageml.c:726: error: syntax error before "R_ExternalPtrAddr"
rmageml.c: In function `getVoidVoid':
rmageml.c:741: error: syntax error before "cls"
rmageml.c:745: error: syntax error before ')' token
rmageml.c:746: error: syntax error before ')' token
rmageml.c:749: 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/Rinst481259649/RMAGEML'
 ERROR
Installation failed.
Removing 'D:/biocbld/bbs-2.1-bioc/tmpdir/Rinst481259649'