##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affyio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affyio_1.76.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affyio’ can be installed ... WARNING
Found the following significant warnings:
  read_abatch.c:656:207: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:656:212: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:665:177: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:665:182: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:677:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:689:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:764:209: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:764:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:774:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:774:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:785:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:785:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:795:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:795:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:805:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:805:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:870:209: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:870:214: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:879:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:879:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:890:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:890:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:901:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:901:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:913:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:913:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:924:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:924:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1567:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1567:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1578:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1578:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1589:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1589:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1665:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1665:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1677:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1677:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1689:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1689:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1701:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1701:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1769:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1769:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1780:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1780:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1791:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1791:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1801:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1801:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_abatch.c:1811:176: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  read_abatch.c:1811:181: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
  read_bpmap.c:849:42: warning: format specifies type 'char *' but the argument has type 'SEXP' (aka 'struct SEXPREC *') [-Wformat]
  read_generic.c:1293:42: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
  read_generic.c:1293:42: warning: variable 'temp32' is uninitialized when used here [-Wuninitialized]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/affyio/libs/affyio.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

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

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

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/affyio.Rcheck/00check.log’
for details.