##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:affyio.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings affyio_1.73.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/affyio.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyio/DESCRIPTION’ ... OK
* this is package ‘affyio’ version ‘1.73.0’
* 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 ... WARNING
Found the following significant warnings:
  read_abatch.c:656:176: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:656:182: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:665:146: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:665:152: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:677:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:677:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:689:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:689:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:764:178: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:764:184: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:774:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:774:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:785:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:785:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:795:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:795:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:805:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:805:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:870:178: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:870:184: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:879:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:879:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:890:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:890:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:901:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:901:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:913:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:913:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:924:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:924:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1567:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1567:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1578:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1578:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1589:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1589:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1665:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1665:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1677:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1677:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1689:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1689:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1701:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1701:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1769:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1769:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1780:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1780:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1791:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1791:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1801:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1801:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1811:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:1811:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  read_abatch.c:3410:3: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  read_abatch.c:2661:3: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  read_bpmap.c:849:39: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=]
  read_bpmap.c:698:20: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  read_bpmap.c:655:20: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  read_bpmap.c:603:18: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  read_celfile_generic.c:272:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:294:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:315:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:336:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:357:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:378:3: warning: ‘strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:399:3: warning: ‘strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:420:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:441:3: warning: ‘strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:464:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:488:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:510:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:532:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:553:3: warning: ‘strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:575:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:597:3: warning: ‘strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1270:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1292:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1313:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1334:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1355:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1376:3: warning: ‘strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1397:3: warning: ‘strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1418:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1439:3: warning: ‘strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1462:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1486:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1508:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1530:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1551:3: warning: ‘strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1573:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  read_celfile_generic.c:1595:3: warning: ‘strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
  read_generic.c:1293:37: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘int’ [-Wformat=]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/affyio.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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 ... OK
* 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/affyio/libs/affyio.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/affyio.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL affyio
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘affyio’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
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... /usr/bin/grep
checking for egrep... /usr/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: Enabling threading for affyio
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c fread_functions.c -o fread_functions.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c init_package.c -o init_package.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_abatch.c -o read_abatch.o
read_abatch.c: In function ‘read_cel_file_intensities’:
read_abatch.c:656:176: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  656 |       Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
      |                                                                                                                                                                               ~^                              ~~~
      |                                                                                                                                                                                |                               |
      |                                                                                                                                                                                int                             size_t {aka long unsigned int}
      |                                                                                                                                                                               %ld
read_abatch.c:656:182: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  656 |       Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
      |                                                                                                                                                                                     ~^                             ~
      |                                                                                                                                                                                      |                             |
      |                                                                                                                                                                                      int                           size_t {aka long unsigned int}
      |                                                                                                                                                                                     %ld
read_abatch.c:665:146: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  665 |        Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                 ~^                              ~~~
      |                                                                                                                                                  |                               |
      |                                                                                                                                                  int                             size_t {aka long unsigned int}
      |                                                                                                                                                 %ld
read_abatch.c:665:152: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  665 |        Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                       ~^                             ~~~~
      |                                                                                                                                                        |                             |
      |                                                                                                                                                        int                           size_t {aka long unsigned int}
      |                                                                                                                                                       %ld
read_abatch.c:677:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  677 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:677:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  677 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:689:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  689 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:689:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  689 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c: In function ‘read_cel_file_stddev’:
read_abatch.c:764:178: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  764 |       Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
      |                                                                                                                                                                                 ~^                              ~~~
      |                                                                                                                                                                                  |                               |
      |                                                                                                                                                                                  int                             size_t {aka long unsigned int}
      |                                                                                                                                                                                 %ld
read_abatch.c:764:184: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  764 |       Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
      |                                                                                                                                                                                       ~^                             ~
      |                                                                                                                                                                                        |                             |
      |                                                                                                                                                                                        int                           size_t {aka long unsigned int}
      |                                                                                                                                                                                       %ld
read_abatch.c:774:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  774 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:774:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  774 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:785:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  785 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:785:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  785 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:795:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  795 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:795:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  795 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:805:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  805 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:805:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  805 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c: In function ‘read_cel_file_npixels’:
read_abatch.c:870:178: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  870 |       Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
      |                                                                                                                                                                                 ~^                              ~~~
      |                                                                                                                                                                                  |                               |
      |                                                                                                                                                                                  int                             size_t {aka long unsigned int}
      |                                                                                                                                                                                 %ld
read_abatch.c:870:184: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  870 |       Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i);
      |                                                                                                                                                                                       ~^                             ~
      |                                                                                                                                                                                        |                             |
      |                                                                                                                                                                                        int                           size_t {aka long unsigned int}
      |                                                                                                                                                                                       %ld
read_abatch.c:879:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  879 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:879:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  879 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:890:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  890 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:890:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  890 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:901:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  901 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:901:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  901 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:913:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  913 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:913:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  913 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:924:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  924 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:924:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  924 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c: In function ‘read_gzcel_file_intensities’:
read_abatch.c:1567:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1567 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1567:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1567 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1578:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1578 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1578:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1578 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1589:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1589 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1589:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1589 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c: In function ‘read_gzcel_file_stddev’:
read_abatch.c:1665:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1665 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1665:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1665 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1677:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1677 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1677:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1677 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1689:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1689 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1689:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1689 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1701:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1701 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1701:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1701 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c: In function ‘read_gzcel_file_npixels’:
read_abatch.c:1769:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1769 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1769:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1769 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1780:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1780 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1780:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1780 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1791:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1791 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1791:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1791 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1801:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1801 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1801:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1801 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c:1811:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1811 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                ~^                              ~~~
      |                                                                                                                                                 |                               |
      |                                                                                                                                                 int                             size_t {aka long unsigned int}
      |                                                                                                                                                %ld
read_abatch.c:1811:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
 1811 |       Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows);
      |                                                                                                                                                      ~^                             ~~~~
      |                                                                                                                                                       |                             |
      |                                                                                                                                                       int                           size_t {aka long unsigned int}
      |                                                                                                                                                      %ld
read_abatch.c: In function ‘gzbinary_get_detailed_header_info’:
read_abatch.c:3410:3: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
 3410 |   strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_abatch.c:3410:65: note: length computed here
 3410 |   strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
      |                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_abatch.c: In function ‘binary_get_detailed_header_info’:
read_abatch.c:2661:3: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
 2661 |   strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_abatch.c:2661:65: note: length computed here
 2661 |   strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1);
      |                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’:
read_bpmap.c:849:39: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=]
  849 |       error("Unable to open the file %s",filename);
      |                                      ~^  ~~~~~~~~
      |                                       |  |
      |                                       |  SEXP {aka struct SEXPREC *}
      |                                       char *
read_bpmap.c:698:20: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  698 |    sprintf(buf, "%d", j+1);
      |                    ^
read_bpmap.c:698:4: note: ‘sprintf’ output between 2 and 11 bytes into a destination of size 10
  698 |    sprintf(buf, "%d", j+1);
      |    ^~~~~~~~~~~~~~~~~~~~~~~
read_bpmap.c:655:20: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  655 |    sprintf(buf, "%d", j+1);
      |                    ^
read_bpmap.c:655:4: note: ‘sprintf’ output between 2 and 11 bytes into a destination of size 10
  655 |    sprintf(buf, "%d", j+1);
      |    ^~~~~~~~~~~~~~~~~~~~~~~
read_bpmap.c:603:18: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  603 |  sprintf(buf, "%d", j+1);
      |                  ^
read_bpmap.c:603:2: note: ‘sprintf’ output between 2 and 11 bytes into a destination of size 10
  603 |  sprintf(buf, "%d", j+1);
      |  ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_cdf_xda.c -o read_cdf_xda.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_cdffile2.c -o read_cdffile2.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function ‘generic_get_detailed_header_info’:
read_celfile_generic.c:272:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  272 |   strncpy(header_info->AlgorithmParameters,"Percentile:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:294:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  294 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:315:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
  315 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:336:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  336 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:357:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  357 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:378:3: warning: ‘strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
  378 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:399:3: warning: ‘strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
  399 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:420:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
  420 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:441:3: warning: ‘strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
  441 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:464:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
  464 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:488:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
  488 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:510:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
  510 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:532:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
  532 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:553:3: warning: ‘strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
  553 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:575:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
  575 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:597:3: warning: ‘strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
  597 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c: In function ‘gzgeneric_get_detailed_header_info’:
read_celfile_generic.c:1270:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
 1270 |   strncpy(header_info->AlgorithmParameters,"Percentile:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1292:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
 1292 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1313:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
 1313 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1334:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
 1334 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1355:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
 1355 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1376:3: warning: ‘strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation]
 1376 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1397:3: warning: ‘strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation]
 1397 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1418:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
 1418 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1439:3: warning: ‘strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation]
 1439 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1462:3: warning: ‘strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation]
 1462 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1486:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
 1486 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1508:3: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
 1508 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1530:3: warning: ‘strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation]
 1530 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1551:3: warning: ‘strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation]
 1551 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1573:3: warning: ‘strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation]
 1573 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_celfile_generic.c:1595:3: warning: ‘strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation]
 1595 |   strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_clf.c -o read_clf.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_generic.c -o read_generic.o
read_generic.c: In function ‘print_decode_nvt_triplet’:
read_generic.c:1293:37: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘int’ [-Wformat=]
 1293 |     Rprintf("Its a float  value is %f\n",temp32);
      |                                    ~^    ~~~~~~
      |                                     |    |
      |                                     |    int
      |                                     double
      |                                    %d
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -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 -Wall   -fPIC  -g -O2  -Wall -c read_pgf.c -o read_pgf.o
read_pgf.c:363:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function]
  363 | static int token_ends_with(char *token, char *ends_in){
      |            ^~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/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 -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-affyio/00new/affyio/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (affyio)