Package: affyio

Version: 1.4.1

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check affyio_1.4.1.tar.gz

RetCode: 0

Time: 62.8 seconds

Status: OK

CheckDir: affyio.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.0-bioc/meat/affyio.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.4.1'
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... 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
* checking for portable use of $BLAS_LIBS ... 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 -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_abatch.c -o read_abatch.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function `ReadBPMAPHeader':
read_bpmap.c:270: warning: unused variable `version_number_int'
read_bpmap.c: At top level:
read_bpmap.c:50: warning: `fread_be_int32' defined but not used
read_bpmap.c:91: warning: `fread_uint32' defined but not used
read_bpmap.c:114: warning: `fread_be_int16' defined but not used
read_bpmap.c:133: warning: `fread_be_uint16' defined but not used
read_bpmap.c:153: warning: `swap_uint_32' defined but not used
read_bpmap.c:180: warning: `fread_be_float32' defined but not used
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c: In function `read_cdf_Units':
read_cdffile2.c:721: warning: statement with no effect
read_cdffile2.c: In function `ReadtextCDFFileIntoRList':
read_cdffile2.c:1040: warning: `QCUNITSProbeInfoX' might be used uninitialized in this function
read_cdffile2.c:1041: warning: `QCUNITSProbeInfoY' might be used uninitialized in this function
read_cdffile2.c:1042: warning: `QCUNITSProbeInfoPROBE' might be used uninitialized in this function
read_cdffile2.c:1043: warning: `QCUNITSProbeInfoPL' might be used uninitialized in this function
read_cdffile2.c:1044: warning: `QCUNITSProbeInfoATOM' might be used uninitialized in this function
read_cdffile2.c:1045: warning: `QCUNITSProbeInfoINDEX' might be used uninitialized in this function
read_cdffile2.c:1046: warning: `QCUNITSProbeInfoPMFLAG' might be used uninitialized in this function
read_cdffile2.c:1047: warning: `QCUNITSProbeInfoBGFLAG' might be used uninitialized in this function
read_cdffile2.c: At top level:
read_cdffile2.c:363: warning: `token_ends_with' defined but not used
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_cdf_xda.c -o read_cdf_xda.o
read_cdf_xda.c:263: warning: `fread_int16' defined but not used
read_cdf_xda.c:301: warning: `swap_float_4' defined but not used
read_cdf_xda.c:309: warning: `fread_float32' defined but not used
gcc -std=gnu99 -shared -L/usr/local/lib -o affyio.so read_abatch.o read_bpmap.o read_cdffile2.o read_cdf_xda.o -lz   -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** 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                      text    html    latex
  read.celfile.header               text    html    latex
  read.celfile.probeintensity.matri text    html    latex
** building package indices ...
* DONE (affyio)