Ben Bolstad
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/affyio |
| Branch: RELEASE_3_10 |
| Last Commit: fd0e865 |
| Last Changed Date: 2019-10-29 13:07:22 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:16:39 -0400 (Wed, 15 Apr 2020).
| Package 30/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affyio 1.56.0 Ben Bolstad
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: affyio |
| Version: 1.56.0 |
| 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 |
| StartedAt: 2020-04-14 19:09:12 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 19:09:51 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 39.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### 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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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