Package: affyio

Version: 1.0.0

Command: D:\biocbld\1.8d\R\bin\R.exe CMD check affyio_1.0.0.tar.gz

RetCode: 0

Time: 27.5 seconds

Status: OK

CheckDir: affyio.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.8d/Rpacks/affyio.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.0.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyio' can be installed ... 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 syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* creating affyio-Ex.R ... OK
* checking examples ... OK
* creating affyio-manual.tex ... OK
* checking affyio-manual.tex ... OK

installing R.css in D:/biocbld/1.8d/Rpacks/affyio.Rcheck


---------- 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/1.8d/R/src/extra/zlib -DHAVE_ZLIB  -Id:/biocbld/1.8d/R/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/1.8d/R/src/extra/zlib -DHAVE_ZLIB  -Id:/biocbld/1.8d/R/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/1.8d/R/src/extra/zlib -DHAVE_ZLIB  -Id:/biocbld/1.8d/R/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/1.8d/R/src/extra/zlib -DHAVE_ZLIB  -Id:/biocbld/1.8d/R/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/1.8d/R/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/1.8d/R/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\1.8d\Rpacks\affyio.Rcheck\00_pkg_src\affyio\chm\affyio.chm


Compile time: 0 minutes, 0 seconds
5	Topics
9	Local links
0	Internet links
1	Graphic


Created d:\biocbld\1.8d\Rpacks\affyio.Rcheck\00_pkg_src\affyio\chm\affyio.chm, 18,857 bytes
Compression increased file by 3,631 bytes.
  adding MD5 sums

* DONE (affyio)