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 affyio.Rcheck && mkdir affyio.buildbin-libdir affyio.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyio.buildbin-libdir affyio_1.48.0.tar.gz >affyio.Rcheck\00install.out 2>&1 && cp affyio.Rcheck\00install.out affyio-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affyio.buildbin-libdir --install="check:affyio-install.out" --force-multiarch --no-vignettes --timings affyio_1.48.0.tar.gz |
| StartedAt: 2018-04-11 22:07:40 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:08:22 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 42.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: affyio.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affyio.buildbin-libdir affyio.Rcheck && mkdir affyio.buildbin-libdir affyio.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyio.buildbin-libdir affyio_1.48.0.tar.gz >affyio.Rcheck\00install.out 2>&1 && cp affyio.Rcheck\00install.out affyio-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affyio.buildbin-libdir --install="check:affyio-install.out" --force-multiarch --no-vignettes --timings affyio_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affyio.Rcheck' * using R version 3.4.4 (2018-03-15) * 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 '1.48.0' * 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 ... OK * 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-3.6-bioc/meat/affyio.buildbin-libdir/affyio/libs/i386/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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affyio.Rcheck/00check.log' for details.
affyio.Rcheck/00install.out
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