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###
### Running command:
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### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL affyio
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* installing to library 'E:/biocbuild/bbs-3.21-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) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: fread_functions.o:fread_function:(.text+0x306): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: fread_functions.o:fread_function:(.text+0x336): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: fread_functions.o:fread_function:(.text+0x362): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: fread_functions.o:fread_function:(.text+0x382): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: fread_functions.o:fread_function:(.text+0x3a6): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: fread_functions.o:fread_function:(.text+0x3d1): more undefined references to `gzread' follow
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x481): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x4cd): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x4e4): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x53a): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x62a): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x744): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x99d): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x9e4): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x9ff): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xa0c): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xae4): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xaff): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xb2c): undefined reference to `gzrewind'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xca9): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xded): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xefd): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0xf56): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x1021): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x10f7): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x1230): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x126f): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x13db): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x141f): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x1f24): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x2044): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x2164): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x2599): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x2b70): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x35f8): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x36ee): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x375d): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x377e): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x433e): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x43b6): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x46c1): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x4736): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x4c79): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x4cf6): more undefined references to `gzclose' follow
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x820a): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_abatch.o:read_abatch.c:(.text+0x831b): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x2864): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x28b6): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x28dc): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x2924): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x2ac5): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x2b19): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x428d): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x45b1): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4796): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4810): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x48ac): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4910): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x496b): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x49e4): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4a30): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4a8b): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4aad): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4b30): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4b8f): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4bea): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4c0c): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4c2e): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4ce8): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4da1): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4dfc): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4eca): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4eef): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4f14): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4f44): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_celfile_generic.o:read_celfile_generic.c:(.text+0x4f86): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_generic.o:read_generic.c:(.text+0x3605): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_generic.o:read_generic.c:(.text+0x3684): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_generic.o:read_generic.c:(.text+0x36a6): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_generic.o:read_generic.c:(.text+0x36be): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_generic.o:read_generic.c:(.text+0x3abf): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_generic.o:read_generic.c:(.text+0x3d97): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xd34): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xd86): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xdac): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xdee): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xe58): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xf14): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xf6a): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0xfc9): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x101f): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x107a): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x10d9): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1163): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x11ca): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1229): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1260): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x12e3): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x133a): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1399): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x13d0): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x13f2): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1475): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x14ce): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x152a): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1561): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1583): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x15a5): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1668): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1729): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x178c): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x185a): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x187f): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x18a4): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x18d4): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: read_multichannel_celfile_generic.o:read_multichannel_celfile_generic.c:(.text+0x1916): undefined reference to `gzclose'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'affyio'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/affyio'
* restoring previous 'E:/biocbuild/bbs-3.21-bioc/R/library/affyio'
