Package: affyio

Version: 1.56.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyio.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings affyio_1.56.0.tar.gz

StartedAt: 2020-04-15 01:11:33 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:11:57 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 24.4 seconds

RetCode: 0

Status:  OK

CheckDir: affyio.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyio.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings affyio_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/affyio.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.56.0'
* 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 ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/affyio/libs/i386/affyio.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/affyio/libs/x64/affyio.dll':
  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. 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/affyio.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/affyio_1.56.0.tar.gz && rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyio.buildbin-libdir affyio_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL affyio_1.56.0.zip && rm affyio_1.56.0.tar.gz affyio_1.56.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  108k  100  108k    0     0  2627k      0 --:--:-- --:--:-- --:--:-- 2853k

install for i386

* installing *source* package 'affyio' ...
** using staged installation

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


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fread_functions.c -o fread_functions.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_abatch.c -o read_abatch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_bpmap.c -o read_bpmap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_cdffile2.c -o read_cdffile2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_celfile_generic.c -o read_celfile_generic.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_clf.c -o read_clf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_generic.c -o read_generic.o
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:2030:2: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SET_VECTOR_ELT(VECTOR_ELT(temp_sxp2,2),i,generic_data_set_rows_R_List(&my_data_set, i));
  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_pgf.c -o read_pgf.o
read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
 static int token_ends_with(char *token, char *ends_in){
            ^
C:/Rtools/mingw_32/bin/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-3.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/affyio.buildbin-libdir/00LOCK-affyio/00new/affyio/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affyio'
    finding HTML links ... done
    check.cdf.type                          html  
    get.celfile.dates                       html  
    read.cdffile.list                       html  
    read.celfile                            html  
    read.celfile.header                     html  
    read.celfile.probeintensity.matrices    html  
    read_abatch                             html  
** 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

install for x64

* installing *source* package 'affyio' ...

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


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fread_functions.c -o fread_functions.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init_package.c -o init_package.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_abatch.c -o read_abatch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:110:18: warning: overflow in implicit constant conversion [-Woverflow]
     fseek(infile,-sizeof(float),SEEK_CUR);
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_cdf_xda.c -o read_cdf_xda.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_cdffile2.c -o read_cdffile2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_celfile_generic.c -o read_celfile_generic.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_clf.c -o read_clf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_generic.c -o read_generic.o
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:2030:2: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SET_VECTOR_ELT(VECTOR_ELT(temp_sxp2,2),i,generic_data_set_rows_R_List(&my_data_set, i));
  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_pgf.c -o read_pgf.o
read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
 static int token_ends_with(char *token, char *ends_in){
            ^
C:/Rtools/mingw_64/bin/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-3.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.56.0.zip
* DONE (affyio)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'affyio' successfully unpacked and MD5 sums checked