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This page was generated on 2024-07-16 11:39 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 28/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyio 1.75.0  (landing page)
Ben Bolstad
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/affyio
git_branch: devel
git_last_commit: a03ad7f
git_last_commit_date: 2024-04-30 10:11:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for affyio on palomino6

To the developers/maintainers of the affyio package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyio.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: affyio
Version: 1.75.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:affyio.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings affyio_1.75.0.tar.gz
StartedAt: 2024-07-15 21:38:16 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 21:38:45 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 29.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: affyio.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:affyio.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings affyio_1.75.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.75.0'
* 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 long unsigned int'} [-Wformat=]
  read_abatch.c:2661:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
  read_abatch.c:3410:3: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation]
  read_bpmap.c:110:18: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551612' to '-4' [-Woverflow]
  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:698:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  read_bpmap.c:655:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  read_bpmap.c:603:25: 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 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 ... OK
* 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 ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/affyio/libs/x64/affyio.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00check.log'
for details.


Installation output

affyio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL affyio
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'affyio' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fread_functions.c -o fread_functions.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init_package.c -o init_package.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 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 long unsigned int}
      |                                                                                                                                                                               %lld
read_abatch.c:656:182: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                                                     %lld
read_abatch.c:665:146: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                 %lld
read_abatch.c:665:152: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                       %lld
read_abatch.c:677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
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 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 long unsigned int}
      |                                                                                                                                                                                 %lld
read_abatch.c:764:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                                                       %lld
read_abatch.c:774:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:774:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:785:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:785:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:795:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:795:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:805:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:805:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
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 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 long unsigned int}
      |                                                                                                                                                                                 %lld
read_abatch.c:870:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                                                       %lld
read_abatch.c:879:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:879:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:890:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:890:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:901:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:901:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:913:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:913:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:924:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:924:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
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 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1567:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1578:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1578:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1589:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1589:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
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 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1665:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1701:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1701:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
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 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1769:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1780:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1780:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1791:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1791:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1801:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1801:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
read_abatch.c:1811:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                %lld
read_abatch.c:1811:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long 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 long unsigned int}
      |                                                                                                                                                      %lld
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-truncation]
 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);
      |                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-truncation]
 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);
      |                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:110:18: warning: overflow in conversion from 'long long unsigned int' to 'long int' changes value from '18446744073709551612' to '-4' [-Woverflow]
  110 |     fseek(infile,-sizeof(float),SEEK_CUR);
      |                  ^~~~~~~~~~~~~~
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:698:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  698 |           sprintf(buf, "%d", j+1);
      |                           ^
In function 'readBPMAPSeqIdPositionInfo',
    inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3:
read_bpmap.c:698:11: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10
  698 |           sprintf(buf, "%d", j+1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~
read_bpmap.c: In function 'ReadBPMAPFileIntoRList':
read_bpmap.c:655:27: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  655 |           sprintf(buf, "%d", j+1);
      |                           ^
In function 'readBPMAPSeqIdPositionInfo',
    inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3:
read_bpmap.c:655:11: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10
  655 |           sprintf(buf, "%d", j+1);
      |           ^~~~~~~~~~~~~~~~~~~~~~~
read_bpmap.c: In function 'ReadBPMAPFileIntoRList':
read_bpmap.c:603:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  603 |         sprintf(buf, "%d", j+1);
      |                         ^
In function 'readBPMAPSeqIdPositionInfo',
    inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3:
read_bpmap.c:603:9: note: 'sprintf' output between 2 and 11 bytes into a destination of size 10
  603 |         sprintf(buf, "%d", j+1);
      |         ^~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_cdf_xda.c -o read_cdf_xda.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_cdffile2.c -o read_cdffile2.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_clf.c -o read_clf.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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
read_generic.c:1293:5: warning: 'temp32' may be used uninitialized [-Wmaybe-uninitialized]
 1293 |     Rprintf("Its a float  value is %f\n",temp32);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
read_generic.c:1283:7: note: 'temp32' declared here
 1283 |   int temp32;
      |       ^~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 -s -static-libgcc -o affyio.dll tmp.def 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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-affyio/00new/affyio/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (affyio)

Tests output


Example timings