BioC 3.5: CHECK report for affyio on malbec2

Package: affyio

Version: 1.46.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings affyio_1.46.0.tar.gz

StartedAt: 2017-08-15 21:02:49 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:03:08 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 18.9 seconds

RetCode: 0

Status:  OK

CheckDir: affyio.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings affyio_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/affyio.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyio/DESCRIPTION’ ... OK
* this is package ‘affyio’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affyio’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... NOTE
read.celfile.header: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/affyio.Rcheck/00check.log’
for details.

* 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 -I/home/biocbuild/bbs-3.5-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:414:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:439:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:458:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
    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 {aka struct gzFile_s *}’ 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:476:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
    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 {aka struct gzFile_s *}’ 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:497:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:513:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:529:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:547:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:575:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:600:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:620:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
    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 {aka struct gzFile_s *}’ 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:636:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
    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 {aka struct gzFile_s *}’ 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:656:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:673:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:690:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:706:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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 -I/home/biocbuild/bbs-3.5-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 -I/home/biocbuild/bbs-3.5-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 [-Wincompatible-pointer-types]
   currentFile = open_gz_cel_file(filename);
               ^
read_abatch.c:1991:22: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzAdvanceToSection(currentFile,"[HEADER]",buffer);
                      ^
read_abatch.c:1439:13: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
             ^
read_abatch.c:1993:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"Cols",buffer);  
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:1998:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"Rows",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2003:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"GridCornerUL",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2009:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"GridCornerUR",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2015:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"GridCornerLR",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2021:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"GridCornerLL",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2027:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"DatHeader",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2059:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"Algorithm",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2067:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"AlgorithmParameters",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2072:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   currentFile = open_gz_cel_file(filename);
               ^
read_abatch.c:2104:22: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzAdvanceToSection(currentFile,"[MASKS]",buffer);
                      ^
read_abatch.c:1439:13: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
             ^
read_abatch.c:2105:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"NumberCells=",buffer); 
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2109:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"CellHeader=",buffer); 
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2118:38: warning: passing argument 3 of ‘ReadgzFileLine’ from incompatible pointer type [-Wincompatible-pointer-types]
     ReadgzFileLine(buffer, BUF_SIZE, currentFile);
                                      ^
read_abatch.c:1354:13: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
             ^
read_abatch.c:2133:22: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzAdvanceToSection(currentFile,"[OUTLIERS]",buffer);
                      ^
read_abatch.c:1439:13: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
             ^
read_abatch.c:2134:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"NumberCells=",buffer);
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2138:20: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzfindStartsWith(currentFile,"CellHeader=",buffer); 
                    ^
read_abatch.c:1416:14: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void  gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
              ^
read_abatch.c:2146:38: warning: passing argument 3 of ‘ReadgzFileLine’ from incompatible pointer type [-Wincompatible-pointer-types]
     ReadgzFileLine(buffer, BUF_SIZE, currentFile);      
                                      ^
read_abatch.c:1354:13: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
             ^
read_abatch.c:2158:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_abatch.c:3148:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3153:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3159:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3164:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3169:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_abatch.c:3247:15: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_abatch.c:3289:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:3591:10: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3597:10: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  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 {aka struct gzFile_s *}’ but argument is of type ‘FILE * {aka struct _IO_FILE *}’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3607:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:3644:10: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3654:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:3692:10: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  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 {aka struct gzFile_s *}’ but argument is of type ‘FILE * {aka struct _IO_FILE *}’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_abatch.c:3702:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:3735:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘FILE * {aka struct _IO_FILE *}’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_abatch.c:3748:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_abatch.c:3761:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_abatch.c:3764:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:3797:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_abatch.c:3827:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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 -I/home/biocbuild/bbs-3.5-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 -I/home/biocbuild/bbs-3.5-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 -I/home/biocbuild/bbs-3.5-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 -I/home/biocbuild/bbs-3.5-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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1074:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     gzclose(infile);
             ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_celfile_generic.c:1080:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     gzclose(infile);
             ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_celfile_generic.c:1089:12: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
    gzclose(infile);
            ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_celfile_generic.c:1094:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1151:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1633:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1701:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1745:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1790:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1802:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1844:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1848:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1861:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:1910:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1915:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1920:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1939:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:1960:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_celfile_generic.c:2012:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:2017:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:2022:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:2038:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
    ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
                            ^
read_celfile_generic.c:2056:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 -I/home/biocbuild/bbs-3.5-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 -I/home/biocbuild/bbs-3.5-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:927:9: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
  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 {aka struct gzFile_s *}’ 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:973:9: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
  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 {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(cur_file_name, "rb")) == NULL)
               ^
read_generic.c:1540:14: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
       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 {aka struct gzFile_s *}’ 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:1683:9: warning: ‘return_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return(return_value);
         ^
read_generic.c: In function ‘Read_Generic_R_List’:
read_generic.c:2029:2: 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:1794:3: 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 -I/home/biocbuild/bbs-3.5-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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:627:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     gzclose(infile);
             ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_multichannel_celfile_generic.c:633:13: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
     gzclose(infile);
             ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_multichannel_celfile_generic.c:642:12: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
    gzclose(infile);
            ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
read_multichannel_celfile_generic.c:647:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:701:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:704:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:741:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:751:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:793:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:807:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:849:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:856:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:867:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:912:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:919:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:923:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:936:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:981:12: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
     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 {aka struct gzFile_s *}’ 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:989:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:994:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:999:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:1018:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:1039:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 [-Wincompatible-pointer-types]
   if ((infile = gzopen(filename, "rb")) == NULL)
               ^
read_multichannel_celfile_generic.c:1090:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:1095:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:1100:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:1116:10: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [-Wincompatible-pointer-types]
   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 {aka struct gzFile_s *}’ 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:1134:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(infile);
           ^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ 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 -I/home/biocbuild/bbs-3.5-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 [-Wincompatible-pointer-types]
  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 -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)