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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:affyio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings affyio_1.76.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.76.0'
* 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 'F:/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 'F:/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
  'F:/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00check.log'
for details.