* installing *source* package ‘affyio’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c fread_functions.c -o fread_functions.o
fread_functions.c: In function ‘gzread_int32’:
fread_functions.c:414:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_uint32’:
fread_functions.c:439:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_int16’:
fread_functions.c:458:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_uint16’:
fread_functions.c:476:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_float32’:
fread_functions.c:497:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(float)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_char’:
fread_functions.c:513:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_uchar’:
fread_functions.c:529:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_double64’:
fread_functions.c:547:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream, destination,sizeof(double)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_int32’:
fread_functions.c:575:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_uint32’:
fread_functions.c:600:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_int16’:
fread_functions.c:620:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_uint16’:
fread_functions.c:636:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_float32’:
fread_functions.c:656:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(float)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_char’:
fread_functions.c:673:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_uchar’:
fread_functions.c:690:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_double64’:
fread_functions.c:706:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream, destination,sizeof(double)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: At top level:
fread_functions.c:300:13: warning: ‘swap_uint_32’ defined but not used [-Wunused-function]
static void swap_uint_32(unsigned int *tni4) /* 4 byte integer numbers */
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c init_package.c -o init_package.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_abatch.c -o read_abatch.o
read_abatch.c: In function ‘read_cel_file_stddev’:
read_abatch.c:735:10: warning: variable ‘cur_mean’ set but not used [-Wunused-but-set-variable]
double cur_mean, cur_stddev;
^
read_abatch.c: In function ‘read_cel_file_npixels’:
read_abatch.c:841:20: warning: variable ‘cur_stddev’ set but not used [-Wunused-but-set-variable]
double cur_mean, cur_stddev;
^
read_abatch.c:841:10: warning: variable ‘cur_mean’ set but not used [-Wunused-but-set-variable]
double cur_mean, cur_stddev;
^
read_abatch.c: In function ‘read_gzcel_file_stddev’:
read_abatch.c:1630:10: warning: variable ‘cur_mean’ set but not used [-Wunused-but-set-variable]
double cur_mean, cur_stddev;
^
read_abatch.c: In function ‘read_gzcel_file_npixels’:
read_abatch.c:1735:20: warning: variable ‘cur_stddev’ set but not used [-Wunused-but-set-variable]
double cur_mean, cur_stddev;
^
read_abatch.c:1735:10: warning: variable ‘cur_mean’ set but not used [-Wunused-but-set-variable]
double cur_mean, cur_stddev;
^
read_abatch.c: In function ‘gz_get_detailed_header_info’:
read_abatch.c:1989:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:1991:3: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [enabled by default]
gzAdvanceToSection(currentFile,"[HEADER]",buffer);
^
read_abatch.c:1439:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:1993:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"Cols",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:1998:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"Rows",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2003:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerUL",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2009:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerUR",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2015:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerLR",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2021:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerLL",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2027:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"DatHeader",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2059:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"Algorithm",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2067:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"AlgorithmParameters",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2072:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(currentFile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gz_get_masks_outliers’:
read_abatch.c:2100:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:2104:3: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [enabled by default]
gzAdvanceToSection(currentFile,"[MASKS]",buffer);
^
read_abatch.c:1439:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:2105:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2109:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2118:5: warning: passing argument 3 of ‘ReadgzFileLine’ from incompatible pointer type [enabled by default]
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^
read_abatch.c:1354:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^
read_abatch.c:2133:3: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [enabled by default]
gzAdvanceToSection(currentFile,"[OUTLIERS]",buffer);
^
read_abatch.c:1439:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:2134:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2138:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2146:5: warning: passing argument 3 of ‘ReadgzFileLine’ from incompatible pointer type [enabled by default]
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^
read_abatch.c:1354:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^
read_abatch.c:2158:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(currentFile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘isgzBinaryCelFile’:
read_abatch.c:3141:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3148:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3153:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3159:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3164:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3169:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binary_header’:
read_abatch.c:3192:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3247:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
if (!gzread(infile,this_header->header,sizeof(char)*this_header->header_len)){
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_abatch.c:3289:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binarycel_file_intensities’:
read_abatch.c:3591:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3597:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct FILE *’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3607:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binarycel_file_stddev’:
read_abatch.c:3644:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3654:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binarycel_file_npixels’:
read_abatch.c:3692:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct FILE *’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3702:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gz_binary_apply_masks’:
read_abatch.c:3735:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->infile,my_header->n_cells*sizeofrecords,SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct FILE *’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3748:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->gzinfile,my_header->n_masks*sizeof(cur_loc),SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3761:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->gzinfile,my_header->n_outliers*sizeof(cur_loc),SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3764:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzbinary_get_masks_outliers’:
read_abatch.c:3797:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->gzinfile,my_header->n_cells*sizeofrecords,SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3827:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘readfile_group’:
read_abatch.c:4369:9: warning: unused variable ‘Current_intensity’ [-Wunused-variable]
SEXP Current_intensity;
^
read_abatch.c: In function ‘read_probeintensities’:
read_abatch.c:4438:11: warning: variable ‘CurintensityMatrix’ set but not used [-Wunused-but-set-variable]
double *CurintensityMatrix, *pmMatrix=0, *mmMatrix=0;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function ‘ReadBPMAPHeader’:
read_bpmap.c:78:7: warning: unused variable ‘version_number_int’ [-Wunused-variable]
int version_number_int;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_cdf_xda.c -o read_cdf_xda.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function ‘read_genericcel_file_intensities’:
read_celfile_generic.c:711:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:709:10: warning: unused variable ‘cur_index’ [-Wunused-variable]
size_t cur_index;
^
read_celfile_generic.c:708:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘read_genericcel_file_stddev’:
read_celfile_generic.c:761:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:759:10: warning: unused variable ‘cur_index’ [-Wunused-variable]
size_t cur_index;
^
read_celfile_generic.c:758:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘read_genericcel_file_npixels’:
read_celfile_generic.c:815:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:813:10: warning: unused variable ‘cur_index’ [-Wunused-variable]
size_t cur_index;
^
read_celfile_generic.c:812:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘generic_get_masks_outliers’:
read_celfile_generic.c:877:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:875:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_celfile_generic.c:874:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0;
^
read_celfile_generic.c: In function ‘generic_apply_masks’:
read_celfile_generic.c:969:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:963:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘isgzGenericCelFile’:
read_celfile_generic.c:1067:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1074:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1080:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1089:4: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1094:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzgeneric_get_header_info’:
read_celfile_generic.c:1115:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1151:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzgeneric_get_detailed_header_info’:
read_celfile_generic.c:1175:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1633:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘check_gzgeneric_cel_file’:
read_celfile_generic.c:1661:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1701:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzread_genericcel_file_intensities’:
read_celfile_generic.c:1726:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1745:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1715:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:1713:10: warning: unused variable ‘cur_index’ [-Wunused-variable]
size_t cur_index;
^
read_celfile_generic.c:1712:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘gzread_genericcel_file_stddev’:
read_celfile_generic.c:1777:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1790:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1802:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1766:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:1764:10: warning: unused variable ‘cur_index’ [-Wunused-variable]
size_t cur_index;
^
read_celfile_generic.c:1763:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘gzread_genericcel_file_npixels’:
read_celfile_generic.c:1831:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1844:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1848:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1861:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1820:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:1818:10: warning: unused variable ‘cur_index’ [-Wunused-variable]
size_t cur_index;
^
read_celfile_generic.c:1817:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
read_celfile_generic.c: In function ‘gzgeneric_get_masks_outliers’:
read_celfile_generic.c:1896:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1910:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1915:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1920:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1939:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1960:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1885:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:1883:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_celfile_generic.c:1882:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0;
^
read_celfile_generic.c: In function ‘gzgeneric_apply_masks’:
read_celfile_generic.c:1991:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:2012:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2017:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2022:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2038:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2056:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1977:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_celfile_generic.c:1971:15: warning: unused variable ‘j’ [-Wunused-variable]
size_t i=0, j=0;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_clf.c -o read_clf.o
read_clf.c: In function ‘read_clf_header’:
read_clf.c:557:7: warning: unused variable ‘i’ [-Wunused-variable]
int i;
^
read_clf.c: At top level:
read_clf.c:292:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
^
read_clf.c:389:12: warning: ‘IsCommentLine’ defined but not used [-Wunused-function]
static int IsCommentLine(char *buffer){
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_generic.c -o read_generic.o
read_generic.c: In function ‘gzread_ASTRING_fw’:
read_generic.c:927:2: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(instream, length-destination->len, SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_generic.c: In function ‘gzread_AWSTRING_fw’:
read_generic.c:973:2: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(instream, length-2*destination->len, SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_generic.c: In function ‘gzRead_Generic’:
read_generic.c:1508:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(cur_file_name, "rb")) == NULL)
^
read_generic.c:1540:7: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_generic.c: In function ‘decode_nvt_triplet’:
read_generic.c:1606:8: warning: ‘return_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP return_value;
^
read_generic.c: In function ‘Read_Generic_R_List’:
read_generic.c:2029:16: warning: ‘return_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(VECTOR_ELT(temp_sxp2,2),i,generic_data_set_rows_R_List(&my_data_set, i));
^
read_generic.c:1794:17: warning: ‘tmp_sexp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(return_value,0,tmp_sexp);
^
read_generic.c:1783:8: note: ‘tmp_sexp’ was declared here
SEXP tmp_sexp, return_names;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function ‘multichannel_determine_number_channels’:
read_multichannel_celfile_generic.c:109:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:106:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:105:17: warning: unused variable ‘k’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c:105:7: warning: unused variable ‘i’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘multichannel_determine_channel_name’:
read_multichannel_celfile_generic.c:173:20: warning: unused variable ‘my_data_set’ [-Wunused-variable]
generic_data_set my_data_set;
^
read_multichannel_celfile_generic.c:165:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:162:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:161:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c:161:7: warning: unused variable ‘i’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘read_genericcel_file_intensities_multichannel’:
read_multichannel_celfile_generic.c:223:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:221:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:220:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘read_genericcel_file_stddev_multichannel’:
read_multichannel_celfile_generic.c:280:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:278:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:277:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘read_genericcel_file_npixels_multichannel’:
read_multichannel_celfile_generic.c:344:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:342:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:341:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘generic_get_masks_outliers_multichannel’:
read_multichannel_celfile_generic.c:418:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:416:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:415:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘generic_apply_masks_multichannel’:
read_multichannel_celfile_generic.c:522:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:516:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0;
^
read_multichannel_celfile_generic.c: In function ‘isgzGenericMultiChannelCelFile’:
read_multichannel_celfile_generic.c:620:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:627:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:633:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:642:4: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:647:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzmultichannel_determine_number_channels’:
read_multichannel_celfile_generic.c:677:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:701:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:704:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:664:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:661:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:660:17: warning: unused variable ‘k’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c:660:7: warning: unused variable ‘i’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘gzmultichannel_determine_channel_name’:
read_multichannel_celfile_generic.c:729:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:741:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:751:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:725:20: warning: unused variable ‘my_data_set’ [-Wunused-variable]
generic_data_set my_data_set;
^
read_multichannel_celfile_generic.c:717:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:714:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:713:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c:713:7: warning: unused variable ‘i’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_intensities_multichannel’:
read_multichannel_celfile_generic.c:778:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:793:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:807:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:766:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:764:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:763:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_stddev_multichannel’:
read_multichannel_celfile_generic.c:834:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:849:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:856:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:867:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:822:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:820:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:819:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_npixels_multichannel’:
read_multichannel_celfile_generic.c:896:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:912:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:919:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:923:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:936:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:884:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:882:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:881:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘gzgeneric_get_masks_outliers_multichannel’:
read_multichannel_celfile_generic.c:965:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:981:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:989:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:994:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:999:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1018:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1039:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:953:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:951:7: warning: unused variable ‘cur_index’ [-Wunused-variable]
int cur_index;
^
read_multichannel_celfile_generic.c:950:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0, k=0;
^
read_multichannel_celfile_generic.c: In function ‘gzgeneric_apply_masks_multichannel’:
read_multichannel_celfile_generic.c:1069:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:1090:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1095:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1100:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1116:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1134:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:1055:7: warning: unused variable ‘fread_err’ [-Wunused-variable]
int fread_err=0;
^
read_multichannel_celfile_generic.c:1049:12: warning: unused variable ‘j’ [-Wunused-variable]
int i=0, j=0;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fpic -g -O2 -Wall -c read_pgf.c -o read_pgf.o
read_pgf.c: In function ‘read_pgf_header’:
read_pgf.c:901:7: warning: unused variable ‘i’ [-Wunused-variable]
int i;
^
read_pgf.c: In function ‘insert_level0’:
read_pgf.c:1167:23: warning: unused variable ‘temp_ptr’ [-Wunused-variable]
probeset_list_node *temp_ptr;
^
read_pgf.c: In function ‘pgf_count_probeset_types’:
read_pgf.c:1265:28: warning: assignment from incompatible pointer type [enabled by default]
my_pgf->probesets->current= my_pgf->probesets->current->next;
^
read_pgf.c: At top level:
read_pgf.c:363:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -lpthread -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/affyio.Rcheck/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)
