Ben Bolstad
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/affyio |
| Branch: RELEASE_3_6 |
| Last Commit: 01727a4 |
| Last Changed Date: 2017-10-30 12:38:18 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:17:09 -0400 (Thu, 12 Apr 2018).
| Package 23/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affyio 1.48.0 Ben Bolstad
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: affyio |
| Version: 1.48.0 |
| Command: rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/affyio_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=affyio.buildbin-libdir --merge-multiarch affyio_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL affyio_1.48.0.zip && rm affyio_1.48.0.tar.gz affyio_1.48.0.zip |
| StartedAt: 2018-04-11 18:28:16 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:29:09 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 53.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/affyio_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=affyio.buildbin-libdir --merge-multiarch affyio_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL affyio_1.48.0.zip && rm affyio_1.48.0.tar.gz affyio_1.48.0.zip
###
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install for i386
* installing *source* package 'affyio' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c fread_functions.c -o fread_functions.o
fread_functions.c:300:13: warning: 'swap_uint_32' defined but not used [-Wunused-function]
static void swap_uint_32(unsigned int *tni4) /* 4 byte integer numbers */
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c init_package.c -o init_package.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_abatch.c -o read_abatch.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_bpmap.c -o read_bpmap.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_cdf_xda.c -o read_cdf_xda.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364:12: 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 -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_celfile_generic.c -o read_celfile_generic.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_clf.c -o read_clf.o
read_clf.c:292:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
^
read_clf.c:389:12: warning: 'IsCommentLine' defined but not used [-Wunused-function]
static int IsCommentLine(char *buffer){
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_generic.c -o read_generic.o
read_generic.c: In function 'decode_nvt_triplet':
read_generic.c:1607:8: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP return_value;
^
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));
^
read_generic.c:1795:3: warning: 'tmp_sexp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(return_value,0,tmp_sexp);
^
read_generic.c:1784:8: note: 'tmp_sexp' was declared here
SEXP tmp_sexp, return_names;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type
my_pgf->probesets->current= my_pgf->probesets->current->next;
^
read_pgf.c: At top level:
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/g++ -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-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/affyio.buildbin-libdir/affyio/libs/i386
** R
** preparing 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
In R CMD INSTALL
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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c fread_functions.c -o fread_functions.o
fread_functions.c:300:13: warning: 'swap_uint_32' defined but not used [-Wunused-function]
static void swap_uint_32(unsigned int *tni4) /* 4 byte integer numbers */
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c init_package.c -o init_package.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_abatch.c -o read_abatch.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_cdf_xda.c -o read_cdf_xda.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364:12: 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 -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_celfile_generic.c -o read_celfile_generic.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_clf.c -o read_clf.o
read_clf.c:292:12: warning: 'token_ends_with' defined but not used [-Wunused-function]
static int token_ends_with(char *token, char *ends_in){
^
read_clf.c:389:12: warning: 'IsCommentLine' defined but not used [-Wunused-function]
static int IsCommentLine(char *buffer){
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_generic.c -o read_generic.o
read_generic.c: In function 'decode_nvt_triplet':
read_generic.c:1607:8: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP return_value;
^
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));
^
read_generic.c:1795:3: warning: 'tmp_sexp' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(return_value,0,tmp_sexp);
^
read_generic.c:1784:8: note: 'tmp_sexp' was declared here
SEXP tmp_sexp, return_names;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type
my_pgf->probesets->current= my_pgf->probesets->current->next;
^
read_pgf.c: At top level:
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/g++ -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-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/affyio.buildbin-libdir/affyio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyio' as affyio_1.48.0.zip
* DONE (affyio)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'affyio' successfully unpacked and MD5 sums checked
In R CMD INSTALL