Package: affyio

Version: 1.0.0

Command: /home/biocbuild/1.8d/R/bin/R CMD check affyio_1.0.0.tar.gz

RetCode: 0

Time: 15.8 seconds

Status: OK

CheckDir: affyio.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/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 for sufficient/correct file permissions ... 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 *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -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: 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
read_abatch.c: In function 'ReadHeader':
read_abatch.c:3019: warning: 'ref_dim_2' may be used uninitialized in this function
read_abatch.c:3019: warning: 'ref_dim_1' may be used uninitialized in this function
read_abatch.c: In function 'read_probeintensities':
read_abatch.c:3229: warning: 'PM_intensity' may be used uninitialized in this function
read_abatch.c:3229: warning: 'MM_intensity' may 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
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -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: 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
read_bpmap.c: In function 'readBPMAPSeqIdPositionInfo':
read_bpmap.c:914: warning: control may reach end of non-void function 'packedSeqTobaseStr' being inlined
read_bpmap.c:680: warning: 'Strand' may be used uninitialized in this function
read_bpmap.c:679: warning: 'PMposition' may be used uninitialized in this function
read_bpmap.c:678: warning: 'MatchScore' may be used uninitialized in this function
read_bpmap.c:677: warning: 'probeSeqString' may be used uninitialized in this function
read_bpmap.c:676: warning: 'PMprobeLength' may be used uninitialized in this function
read_bpmap.c:675: warning: 'yMM' may be used uninitialized in this function
read_bpmap.c:675: warning: 'xMM' may be used uninitialized in this function
read_bpmap.c:675: warning: 'yPM' may be used uninitialized in this function
read_bpmap.c:675: warning: 'xPM' may be used uninitialized in this function
read_bpmap.c:671: warning: 'PositionInfo' may be used uninitialized in this function
read_bpmap.c:688: warning: 'probe_mapping_type' may be used uninitialized in this function
read_bpmap.c:687: warning: 'nprobes' may be used uninitialized in this function
read_bpmap.c: In function 'ReadBPMAPFileIntoRList':
read_bpmap.c:317: warning: 'CurSequenceDescription' may be used uninitialized in this function
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -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_unit_block':
read_cdffile2.c:720: warning: statement with no effect
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:980: warning: unused variable 'cur_tokenset'
read_cdffile2.c:978: warning: unused variable 'i'
read_cdffile2.c: At top level:
read_cdffile2.c:362: warning: 'token_ends_with' defined but not used
read_cdffile2.c: In function 'ReadtextCDFFileIntoRList':
read_cdffile2.c:1047: warning: 'QCUNITSProbeInfoNames' may be used uninitialized in this function
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -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:815: warning: unused variable 'Rf_ncols'
read_cdf_xda.c:815: warning: unused variable 'Rf_nrows'
read_cdf_xda.c:808: warning: unused variable 'which_probetype'
read_cdf_xda.c:804: warning: unused variable 'tmp_name'
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
read_cdf_xda.c: In function 'ReadCDFFileIntoRList':
read_cdf_xda.c:1099: warning: 'CDFInfo' may be used uninitialized in this function
read_cdf_xda.c: In function 'ReadCDFFile':
read_cdf_xda.c:798: warning: 'PSnames' may be used uninitialized in this function
read_cdf_xda.c:796: warning: 'LocMap' may be used uninitialized in this function
gcc -shared -L/usr/local/lib64 -o affyio.so read_abatch.o read_bpmap.o read_cdffile2.o read_cdf_xda.o -lz   
** R
** save image
** help
 >>> Building/Updating help pages for package 'affyio'
     Formats: text html latex example 
  check.cdf.type                    text    html    latex
  read.cdffile.list                 text    html    latex
  read.celfile.header               text    html    latex
  read.celfile.probeintensity.matri text    html    latex
** building package indices ...
* DONE (affyio)