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---------- Making package affyio ------------

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

  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making read_abatch.d from read_abatch.c
making read_bpmap.d from read_bpmap.c
making read_cdf_xda.d from read_cdf_xda.c
making read_cdffile2.d from read_cdffile2.c
gcc  -ID:/biocbld/R-2.3.0/src/extra/zlib -DHAVE_ZLIB  -ID:/biocbld/R-2.3.0/include -Wall -O2   -c read_abatch.c -o read_abatch.o
read_abatch.c: In function `get_masks_outliers':
read_abatch.c:864: warning: unused variable `cur_index'
read_abatch.c: In function `gz_get_masks_outliers':
read_abatch.c:1775: warning: unused variable `cur_index'
read_abatch.c: In function `fread_char':
read_abatch.c:2104: warning: unused variable `i'
read_abatch.c: In function `binary_get_detailed_header_info':
read_abatch.c:2384: warning: unused variable `cdfName'
read_abatch.c: In function `binary_get_masks_outliers':
read_abatch.c:2781: warning: unused variable `cur_index'
read_abatch.c: In function `ReadHeader':
read_abatch.c:3027: warning: unused variable `cel_dimensions_names'
read_abatch.c: In function `R_read_cel_file':
read_abatch.c:3872: warning: unused variable `myCEL'
read_abatch.c: In function `read_probeintensities':
read_abatch.c:3229: warning: 'PM_intensity' might be used uninitialized in this function
read_abatch.c:3229: warning: 'MM_intensity' might be used uninitialized in this function
read_abatch.c: In function `read_cel_file':
read_abatch.c:3854: warning: control reaches end of non-void function
read_abatch.c: In function `R_read_cel_file':
read_abatch.c:3877: warning: control reaches end of non-void function
read_abatch.c: At top level:
read_abatch.c:2077: warning: 'swap_float_4' defined but not used
read_abatch.c:2776: warning: 'binary_get_masks_outliers' defined but not used
gcc  -ID:/biocbld/R-2.3.0/src/extra/zlib -DHAVE_ZLIB  -ID:/biocbld/R-2.3.0/include -Wall -O2   -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function `fread_be_char':
read_bpmap.c:184: warning: unused variable `i'
read_bpmap.c: In function `fread_be_uchar':
read_bpmap.c:200: warning: unused variable `i'
read_bpmap.c: In function `readBPMAPSeqIdPositionInfo':
read_bpmap.c:671: warning: 'PositionInfo' might be used uninitialized in this function
read_bpmap.c:675: warning: 'xPM' might be used uninitialized in this function
read_bpmap.c:675: warning: 'yPM' might be used uninitialized in this function
read_bpmap.c:675: warning: 'xMM' might be used uninitialized in this function
read_bpmap.c:675: warning: 'yMM' might be used uninitialized in this function
read_bpmap.c:676: warning: 'PMprobeLength' might be used uninitialized in this function
read_bpmap.c:677: warning: 'probeSeqString' might be used uninitialized in this function
read_bpmap.c:678: warning: 'MatchScore' might be used uninitialized in this function
read_bpmap.c:679: warning: 'PMposition' might be used uninitialized in this function
read_bpmap.c:680: warning: 'Strand' might be used uninitialized in this function
read_bpmap.c:687: warning: 'nprobes' might be used uninitialized in this function
read_bpmap.c:688: warning: 'probe_mapping_type' might be used uninitialized in this function
read_bpmap.c: In function `ReadBPMAPFileIntoRList':
read_bpmap.c:317: warning: 'CurSequenceDescription' might be used uninitialized in this function
read_bpmap.c: At top level:
read_bpmap.c:48: warning: 'fread_be_int32' defined but not used
read_bpmap.c:90: warning: 'fread_be_int16' defined but not used
read_bpmap.c:109: warning: 'fread_be_uint16' defined but not used
gcc  -ID:/biocbld/R-2.3.0/src/extra/zlib -DHAVE_ZLIB  -ID:/biocbld/R-2.3.0/include -Wall -O2   -c read_cdf_xda.c -o read_cdf_xda.o
read_cdf_xda.c: In function `fread_char':
read_cdf_xda.c:325: warning: unused variable `i'
read_cdf_xda.c: In function `fread_uchar':
read_cdf_xda.c:341: warning: unused variable `i'
read_cdf_xda.c: In function `read_cdf_qcunit':
read_cdf_xda.c:374: warning: unused variable `j'
read_cdf_xda.c: In function `check_cdf_xda':
read_cdf_xda.c:678: warning: unused variable `i'
read_cdf_xda.c: In function `ReadCDFFile':
read_cdf_xda.c:804: warning: unused variable `tmp_name'
read_cdf_xda.c:808: warning: unused variable `which_probetype'
read_cdf_xda.c:815: warning: unused variable `Rf_nrows'
read_cdf_xda.c:815: warning: unused variable `Rf_ncols'
read_cdf_xda.c:796: warning: 'LocMap' might be used uninitialized in this function
read_cdf_xda.c:798: warning: 'PSnames' might be used uninitialized in this function
read_cdf_xda.c: In function `ReadCDFFileIntoRList':
read_cdf_xda.c:1099: warning: 'CDFInfo' might be used uninitialized in this function
read_cdf_xda.c: At top level:
read_cdf_xda.c:260: warning: 'fread_int16' defined but not used
read_cdf_xda.c:298: warning: 'swap_float_4' defined but not used
read_cdf_xda.c:306: warning: 'fread_float32' defined but not used
gcc  -ID:/biocbld/R-2.3.0/src/extra/zlib -DHAVE_ZLIB  -ID:/biocbld/R-2.3.0/include -Wall -O2   -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c: In function `read_cdf_QCUnits_probes':
read_cdffile2.c:540: warning: unused variable `j'
read_cdffile2.c: In function `read_cdf_text':
read_cdffile2.c:871: warning: unused variable `i'
read_cdffile2.c: In function `isTextCDFFile':
read_cdffile2.c:978: warning: unused variable `i'
read_cdffile2.c:980: warning: unused variable `cur_tokenset'
read_cdffile2.c: In function `read_cdf_Units':
read_cdffile2.c:720: warning: statement with no effect
read_cdffile2.c: In function `ReadtextCDFFileIntoRList':
read_cdffile2.c:1039: warning: 'QCUNITSProbeInfoX' might be used uninitialized in this function
read_cdffile2.c:1040: warning: 'QCUNITSProbeInfoY' might be used uninitialized in this function
read_cdffile2.c:1041: warning: 'QCUNITSProbeInfoPROBE' might be used uninitialized in this function
read_cdffile2.c:1042: warning: 'QCUNITSProbeInfoPL' might be used uninitialized in this function
read_cdffile2.c:1043: warning: 'QCUNITSProbeInfoATOM' might be used uninitialized in this function
read_cdffile2.c:1044: warning: 'QCUNITSProbeInfoINDEX' might be used uninitialized in this function
read_cdffile2.c:1045: warning: 'QCUNITSProbeInfoPMFLAG' might be used uninitialized in this function
read_cdffile2.c:1046: warning: 'QCUNITSProbeInfoBGFLAG' might be used uninitialized in this function
read_cdffile2.c:1047: warning: 'QCUNITSProbeInfoNames' might be used uninitialized in this function
read_cdffile2.c: At top level:
read_cdffile2.c:362: warning: 'token_ends_with' defined but not used
windres --include-dir D:/biocbld/R-2.3.0/include  -i affyio_res.rc -o affyio_res.o
gcc  -shared -s  -o affyio.dll affyio.def read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o affyio_res.o  -LD:/biocbld/R-2.3.0/bin   -lR
  ... DLL made
  installing DLL
  installing R files
  save image
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'affyio'
     Formats: text html latex example chm 
  check.cdf.type                    text    html    latex           chm
  read.cdffile.list                 text    html    latex           chm
  read.celfile.header               text    html    latex           chm
  read.celfile.probeintensity.matri text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702



Compiling d:\biocbld\work-area\1.8d\madman\Rpacks\R.INSTALL\affyio\chm\affyio.chm





Compile time: 0 minutes, 0 seconds

5	Topics

9	Local links

0	Internet links

1	Graphic





Created d:\biocbld\work-area\1.8d\madman\Rpacks\R.INSTALL\affyio\chm\affyio.chm, 18,857 bytes

Compression increased file by 3,631 bytes.

  adding MD5 sums

packaged installation of package 'affyio' as affyio_1.0.0.zip
* DONE (affyio)