[GenABEL-dev] Error wil testing ProbABEL 0.4.2
Jean Mao
maoj at mail.nih.gov
Mon Mar 3 18:34:28 CET 2014
Hi Lennart,
Thank you very much for your reply. Please see attached log files. I
think 3.0.2 is the version of R I used.
Jean
On 3/3/2014 3:52 AM, L.C. Karssen wrote:
> Dear Jean,
>
> Thank you for you interest in ProbABEL. From the output you sent us, it
> seems that one of the checks fails in which the output of various
> regressions in R are compared to ProbABEL output. (The XFAIL part is an
> expected failure, so only the check for pacoxph fails).
>
> In order to further diagnose the problem, we need some more information.
> Which Linux distribution are you using? Which version of R is installed
> on your machine?
>
> Could you sent us the config.log file that was created when you ran
> ./configure?
>
>
> One last thing that comes to mind: ./configure tests for the existence
> of R, but it doesn't check whether you have the 'survival' R package
> installed. I guess that is the problem here.
>
>
> Best,
>
> Lennart.
>
> On 28-02-14 19:51, Jean Mao wrote:
>> Hi,
>>
>> Thank you very much for providing this software to scientific community.
>> We have installed it in our cluster for NIH scientists.
>>
>> Recently, while trying to update to 0.4.2 version, I ran into error
>> message when testing the installation. Attached is the log file. Any
>> help will be appreciated. Thank you.
>>
>> Jean Mao
>> Helix Staff
>> CIT, NIH
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
-------------- next part --------------
Making all in src
make[1]: Entering directory `/usr/local/apps/probabel/0.4.2/src'
make all-am
make[2]: Entering directory `/usr/local/apps/probabel/0.4.2/src'
CXX palinear-data.o
CXX palinear-gendata.o
CXX palinear-command_line_settings.o
CXX palinear-usage.o
CXX palinear-main.o
CXX palinear-utilities.o
CXX palinear-phedata.o
CXX palinear-cholesky.o
CXX palinear-regdata.o
CXX palinear-maskedmatrix.o
CXX palinear-reg1.o
CXX palinear-main_functions_dump.o
CXX palinear-AbstractMatrix.o
CXX palinear-CastUtils.o
CXX palinear-convert_util.o
CXX palinear-FileVector.o
CXX palinear-FilteredMatrix.o
CXX palinear-frutil.o
CXX palinear-Logger.o
CXX palinear-RealHandlerWrapper.o
CXX palinear-ReusableFileHandle.o
CXX palinear-Transposer.o
CXXLD palinear
CXX palogist-data.o
CXX palogist-gendata.o
CXX palogist-command_line_settings.o
CXX palogist-usage.o
CXX palogist-main.o
CXX palogist-utilities.o
CXX palogist-phedata.o
CXX palogist-cholesky.o
CXX palogist-regdata.o
CXX palogist-maskedmatrix.o
CXX palogist-reg1.o
CXX palogist-main_functions_dump.o
CXX palogist-AbstractMatrix.o
CXX palogist-CastUtils.o
CXX palogist-convert_util.o
CXX palogist-FileVector.o
CXX palogist-FilteredMatrix.o
CXX palogist-frutil.o
CXX palogist-Logger.o
CXX palogist-RealHandlerWrapper.o
CXX palogist-ReusableFileHandle.o
CXX palogist-Transposer.o
CXXLD palogist
CC pacoxph-coxfit2.o
CC pacoxph-chinv2.o
CC pacoxph-cholesky2.o
CC pacoxph-chsolve2.o
CC pacoxph-dmatrix.o
CXX pacoxph-data.o
CXX pacoxph-gendata.o
CXX pacoxph-command_line_settings.o
CXX pacoxph-usage.o
CXX pacoxph-main.o
CXX pacoxph-utilities.o
CXX pacoxph-phedata.o
CXX pacoxph-cholesky.o
CXX pacoxph-regdata.o
CXX pacoxph-maskedmatrix.o
CXX pacoxph-reg1.o
CXX pacoxph-main_functions_dump.o
CXX pacoxph-AbstractMatrix.o
CXX pacoxph-CastUtils.o
CXX pacoxph-convert_util.o
CXX pacoxph-FileVector.o
CXX pacoxph-FilteredMatrix.o
CXX pacoxph-frutil.o
CXX pacoxph-Logger.o
CXX pacoxph-RealHandlerWrapper.o
CXX pacoxph-ReusableFileHandle.o
CXX pacoxph-Transposer.o
CXX pacoxph-coxph_data.o
CXXLD pacoxph
make[2]: Leaving directory `/usr/local/apps/probabel/0.4.2/src'
make[1]: Leaving directory `/usr/local/apps/probabel/0.4.2/src'
Making all in doc
make[1]: Entering directory `/usr/local/apps/probabel/0.4.2/doc'
=== Making ProbABEL_manual.aux file ===
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[] \OT1/cmtt/m/n/12 --mmscore : score test in samples of related indivi
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\OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 takes three files as in-put: a file c
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[3] [4]
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[]\OT1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams
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[5] [6] [7]
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=== Making index ===
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=== Making final PDF ===
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\OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 takes three files as in-put: a file c
on-tain-ing SNP in-for-ma-tion (e.g. the
[3] [4]
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[]\OT1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams
\OT1/cmtt/m/n/12 palinear \OT1/cmr/m/n/12 and \OT1/cmtt/m/n/12 palogist\OT1/cmr
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[5] [6] [7]
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[]\OT1/cmtt/m/n/12 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin,
EMCR[]
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[] \OT1/cmtt/m/n/12 --allcov : report estimates for all covariates (la
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[] \OT1/cmtt/m/n/12 --interaction: Which covariate to use for interacti
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[] \OT1/cmtt/m/n/12 --mmscore : score test in samples of related indivi
duals. File with inverse of variance-covariance matrix (for palinear) or invers
e correlation (for palogist) as input parameter[]
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[] \OT1/cmtt/m/n/12 --robust : report robust (aka sandwich, aka Hubert
-White) standard errors[]
[8]
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[]\OT1/cmr/m/n/12 These op-tions are \OT1/cmtt/m/n/12 --dose \OT1/cmr/m/n/12 (o
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MLDOSE
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[10] [11]
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\OT1/cmr/m/n/12 After in-stalling \OT1/cmtt/m/n/12 ProbABEL \OT1/cmr/m/n/12 you
can find the \OT1/cmtt/m/n/12 prepare[]data.R \OT1/cmr/m/n/12 file in the \OT1
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[12] [13]
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generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --prefix=/usr/local/apps/probabel/0.4.2 --without-eigen
## --------- ##
## Platform. ##
## --------- ##
hostname = biowulf.nih.gov
uname -m = x86_64
uname -r = 2.6.18-371.3.1.el5
uname -s = Linux
uname -v = #1 SMP Mon Nov 11 03:23:58 EST 2013
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/apps/augustus/2.5.5/scripts
PATH: /usr/local/apps/augustus/2.5.5/bin
PATH: /usr/local/pbs/bin
PATH: /usr/local/bin
PATH: /usr/local/mysql/bin
PATH: /usr/X11R6/bin
PATH: /usr/local/jdk/bin
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/sbin
PATH: /usr/local/etc
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/sbin
PATH: /usr/local/etc
PATH: /home/maoj/bin
PATH: /sbin
PATH: /usr/sbin
PATH: /usr/local/sbin
PATH: /usr/local/etc
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2341: checking for a BSD-compatible install
configure:2409: result: /usr/bin/install -c
configure:2420: checking whether build environment is sane
configure:2475: result: yes
configure:2626: checking for a thread-safe mkdir -p
configure:2665: result: /bin/mkdir -p
configure:2672: checking for gawk
configure:2688: found /bin/gawk
configure:2699: result: gawk
configure:2710: checking whether make sets $(MAKE)
configure:2732: result: yes
configure:2761: checking whether make supports nested variables
configure:2778: result: yes
configure:2873: checking whether make supports nested variables
configure:2890: result: yes
configure:2910: checking whether to enable maintainer-specific portions of Makefiles
configure:2919: result: yes
configure:2982: checking for gcc
configure:2998: found /usr/bin/gcc
configure:3009: result: gcc
configure:3238: checking for C compiler version
configure:3247: gcc --version >&5
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3258: $? = 0
configure:3247: gcc -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
configure:3258: $? = 0
configure:3247: gcc -V >&5
gcc: '-V' option must have argument
configure:3258: $? = 1
configure:3247: gcc -qversion >&5
gcc: unrecognized option '-qversion'
gcc: no input files
configure:3258: $? = 1
configure:3278: checking whether the C compiler works
configure:3300: gcc conftest.c >&5
configure:3304: $? = 0
configure:3352: result: yes
configure:3355: checking for C compiler default output file name
configure:3357: result: a.out
configure:3363: checking for suffix of executables
configure:3370: gcc -o conftest conftest.c >&5
configure:3374: $? = 0
configure:3396: result:
configure:3418: checking whether we are cross compiling
configure:3426: gcc -o conftest conftest.c >&5
configure:3430: $? = 0
configure:3437: ./conftest
configure:3441: $? = 0
configure:3456: result: no
configure:3461: checking for suffix of object files
configure:3483: gcc -c conftest.c >&5
configure:3487: $? = 0
configure:3508: result: o
configure:3512: checking whether we are using the GNU C compiler
configure:3531: gcc -c conftest.c >&5
configure:3531: $? = 0
configure:3540: result: yes
configure:3549: checking whether gcc accepts -g
configure:3569: gcc -c -g conftest.c >&5
configure:3569: $? = 0
configure:3610: result: yes
configure:3627: checking for gcc option to accept ISO C89
configure:3690: gcc -c -g -O2 conftest.c >&5
configure:3690: $? = 0
configure:3703: result: none needed
configure:3734: checking for style of include used by make
configure:3762: result: GNU
configure:3788: checking dependency style of gcc
configure:3899: result: gcc3
configure:3915: checking whether gcc and cc understand -c and -o together
configure:3946: gcc -c conftest.c -o conftest2.o >&5
configure:3950: $? = 0
configure:3956: gcc -c conftest.c -o conftest2.o >&5
configure:3960: $? = 0
configure:3971: cc -c conftest.c >&5
configure:3975: $? = 0
configure:3983: cc -c conftest.c -o conftest2.o >&5
configure:3987: $? = 0
configure:3993: cc -c conftest.c -o conftest2.o >&5
configure:3997: $? = 0
configure:4015: result: yes
configure:4041: checking whether ln -s works
configure:4045: result: yes
configure:4120: checking for g++
configure:4136: found /usr/bin/g++
configure:4147: result: g++
configure:4174: checking for C++ compiler version
configure:4183: g++ --version >&5
g++ (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:4194: $? = 0
configure:4183: g++ -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
configure:4194: $? = 0
configure:4183: g++ -V >&5
g++: '-V' option must have argument
configure:4194: $? = 1
configure:4183: g++ -qversion >&5
g++: unrecognized option '-qversion'
g++: no input files
configure:4194: $? = 1
configure:4198: checking whether we are using the GNU C++ compiler
configure:4217: g++ -c -g -O2 -Wall conftest.cpp >&5
configure:4217: $? = 0
configure:4226: result: yes
configure:4235: checking whether g++ accepts -g
configure:4255: g++ -c -g -Wall conftest.cpp >&5
configure:4255: $? = 0
configure:4296: result: yes
configure:4321: checking dependency style of g++
configure:4432: result: gcc3
configure:4471: checking how to run the C++ preprocessor
configure:4498: g++ -E -Wall conftest.cpp
configure:4498: $? = 0
configure:4512: g++ -E -Wall conftest.cpp
conftest.cpp:11:28: error: ac_nonexistent.h: No such file or directory
configure:4512: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ProbABEL"
| #define PACKAGE_TARNAME "probabel"
| #define PACKAGE_VERSION "0.4.2"
| #define PACKAGE_STRING "ProbABEL 0.4.2"
| #define PACKAGE_BUGREPORT "genabel-devel at r-forge.wu-wien.ac.at"
| #define PACKAGE_URL ""
| #define PACKAGE "probabel"
| #define VERSION "0.4.2"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4537: result: g++ -E
configure:4557: g++ -E -Wall conftest.cpp
configure:4557: $? = 0
configure:4571: g++ -E -Wall conftest.cpp
conftest.cpp:11:28: error: ac_nonexistent.h: No such file or directory
configure:4571: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ProbABEL"
| #define PACKAGE_TARNAME "probabel"
| #define PACKAGE_VERSION "0.4.2"
| #define PACKAGE_STRING "ProbABEL 0.4.2"
| #define PACKAGE_BUGREPORT "genabel-devel at r-forge.wu-wien.ac.at"
| #define PACKAGE_URL ""
| #define PACKAGE "probabel"
| #define VERSION "0.4.2"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:4600: checking for grep that handles long lines and -e
configure:4658: result: /bin/grep
configure:4663: checking for egrep
configure:4725: result: /bin/grep -E
configure:4730: checking for ANSI C header files
configure:4750: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4750: $? = 0
configure:4823: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4823: $? = 0
configure:4823: ./conftest
configure:4823: $? = 0
configure:4834: result: yes
configure:4847: checking for sys/types.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for sys/stat.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for stdlib.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for string.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for memory.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for strings.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for inttypes.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for stdint.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4847: checking for unistd.h
configure:4847: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4847: $? = 0
configure:4847: result: yes
configure:4859: checking for size_t
configure:4859: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4859: $? = 0
configure:4859: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:57: error: expected primary-expression before ')' token
configure:4859: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ProbABEL"
| #define PACKAGE_TARNAME "probabel"
| #define PACKAGE_VERSION "0.4.2"
| #define PACKAGE_STRING "ProbABEL 0.4.2"
| #define PACKAGE_BUGREPORT "genabel-devel at r-forge.wu-wien.ac.at"
| #define PACKAGE_URL ""
| #define PACKAGE "probabel"
| #define VERSION "0.4.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:4859: result: yes
configure:4872: checking for working alloca.h
configure:4889: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4889: $? = 0
configure:4897: result: yes
configure:4905: checking for alloca
configure:4942: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:4942: $? = 0
configure:4950: result: yes
configure:5061: checking float.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking float.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for float.h
configure:5061: result: yes
configure:5061: checking for inttypes.h
configure:5061: result: yes
configure:5061: checking libintl.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking libintl.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for libintl.h
configure:5061: result: yes
configure:5061: checking limits.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking limits.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for limits.h
configure:5061: result: yes
configure:5061: checking stddef.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking stddef.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for stddef.h
configure:5061: result: yes
configure:5061: checking for stdint.h
configure:5061: result: yes
configure:5061: checking for stdlib.h
configure:5061: result: yes
configure:5061: checking for string.h
configure:5061: result: yes
configure:5061: checking sys/param.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking sys/param.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for sys/param.h
configure:5061: result: yes
configure:5061: checking wchar.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking wchar.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for wchar.h
configure:5061: result: yes
configure:5061: checking wctype.h usability
configure:5061: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking wctype.h presence
configure:5061: g++ -E -Wall conftest.cpp
configure:5061: $? = 0
configure:5061: result: yes
configure:5061: checking for wctype.h
configure:5061: result: yes
configure:5118: not using Eigen for linear algebra
configure:5132: checking for stdbool.h that conforms to C99
configure:5199: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5199: $? = 0
configure:5206: result: yes
configure:5208: checking for _Bool
configure:5208: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:70: error: '_Bool' was not declared in this scope
configure:5208: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ProbABEL"
| #define PACKAGE_TARNAME "probabel"
| #define PACKAGE_VERSION "0.4.2"
| #define PACKAGE_STRING "ProbABEL 0.4.2"
| #define PACKAGE_BUGREPORT "genabel-devel at r-forge.wu-wien.ac.at"
| #define PACKAGE_URL ""
| #define PACKAGE "probabel"
| #define VERSION "0.4.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ALLOCA_H 1
| #define HAVE_ALLOCA 1
| #define HAVE_FLOAT_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIBINTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_WCHAR_H 1
| #define HAVE_WCTYPE_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof (_Bool))
| return 0;
| ;
| return 0;
| }
configure:5208: result: no
configure:5225: checking for inline
configure:5241: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5241: $? = 0
configure:5249: result: inline
configure:5267: checking for off_t
configure:5267: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5267: $? = 0
configure:5267: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
conftest.cpp: In function 'int main()':
conftest.cpp:71: error: expected primary-expression before ')' token
configure:5267: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ProbABEL"
| #define PACKAGE_TARNAME "probabel"
| #define PACKAGE_VERSION "0.4.2"
| #define PACKAGE_STRING "ProbABEL 0.4.2"
| #define PACKAGE_BUGREPORT "genabel-devel at r-forge.wu-wien.ac.at"
| #define PACKAGE_URL ""
| #define PACKAGE "probabel"
| #define VERSION "0.4.2"
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ALLOCA_H 1
| #define HAVE_ALLOCA 1
| #define HAVE_FLOAT_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_LIBINTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_WCHAR_H 1
| #define HAVE_WCTYPE_H 1
| #define HAVE_STDBOOL_H 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((off_t)))
| return 0;
| ;
| return 0;
| }
configure:5267: result: yes
configure:5278: checking for size_t
configure:5278: result: yes
configure:5291: checking for error_at_line
configure:5307: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5307: $? = 0
configure:5315: result: yes
configure:5331: checking for pow
configure:5331: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5331: $? = 0
configure:5331: result: yes
configure:5331: checking for putenv
configure:5331: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5331: $? = 0
configure:5331: result: yes
configure:5331: checking for sqrt
configure:5331: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5331: $? = 0
configure:5331: result: yes
configure:5331: checking for strdup
configure:5331: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5331: $? = 0
configure:5331: result: yes
configure:5331: checking for strncasecmp
configure:5331: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5331: $? = 0
configure:5331: result: yes
configure:5331: checking for floor
configure:5331: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5331: $? = 0
configure:5331: result: yes
configure:5349: checking for special C compiler options needed for large files
configure:5394: result: no
configure:5400: checking for _FILE_OFFSET_BITS value needed for large files
configure:5425: g++ -c -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5425: $? = 0
configure:5457: result: no
configure:5545: checking for _LARGEFILE_SOURCE value needed for large files
configure:5564: g++ -o conftest -g -O2 -D_NOT_R_FILEVECTOR -Wall conftest.cpp >&5
configure:5564: $? = 0
configure:5592: result: no
configure:5616: checking for a sed that does not truncate output
configure:5680: result: /usr/local/bin/sed
configure:5691: checking for gawk
configure:5718: result: gawk
configure:5733: checking for pdflatex
configure:5763: result: no
configure:5769: WARNING: Unable to create PDF version of the user manual
configure:5784: checking for R
configure:5800: found /usr/local/bin/R
configure:5811: result: R
configure:5843: building of palinear is enabled
configure:5864: building of palogist is enabled
configure:5886: building of pacoxph is enabled
configure:6037: checking that generated files are newer than configure
configure:6043: result: done
configure:6102: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by ProbABEL config.status 0.4.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on biowulf.nih.gov
config.status:906: creating Makefile
config.status:906: creating src/Makefile
config.status:906: creating doc/Makefile
config.status:906: creating examples/Makefile
config.status:906: creating checks/Makefile
config.status:906: creating checks/R-tests/Makefile
config.status:906: creating src/config.h
config.status:1087: src/config.h is unchanged
config.status:1135: executing depfiles commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
ac_cv_c_inline=inline
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func_alloca_works=yes
ac_cv_func_floor=yes
ac_cv_func_pow=yes
ac_cv_func_putenv=yes
ac_cv_func_sqrt=yes
ac_cv_func_strdup=yes
ac_cv_func_strncasecmp=yes
ac_cv_header_float_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_libintl_h=yes
ac_cv_header_limits_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdbool_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stddef_h=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_param_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_header_wchar_h=yes
ac_cv_header_wctype_h=yes
ac_cv_lib_error_at_line=yes
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_SED=/usr/local/bin/sed
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_R=R
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_gcc_c_o=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_sys_file_offset_bits=no
ac_cv_sys_largefile_CC=no
ac_cv_sys_largefile_source=no
ac_cv_type__Bool=no
ac_cv_type_off_t=yes
ac_cv_type_size_t=yes
ac_cv_working_alloca_h=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /usr/local/apps/probabel/0.4.2/missing aclocal-1.13'
ALLOCA=''
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='0'
AM_V='$(V)'
AUTOCONF='${SHELL} /usr/local/apps/probabel/0.4.2/missing autoconf'
AUTOHEADER='${SHELL} /usr/local/apps/probabel/0.4.2/missing autoheader'
AUTOMAKE='${SHELL} /usr/local/apps/probabel/0.4.2/missing automake-1.13'
AWK='gawk'
BUILD_extractsnp_FALSE=''
BUILD_extractsnp_TRUE='#'
BUILD_pacoxph_FALSE='#'
BUILD_pacoxph_TRUE=''
BUILD_palinear_FALSE='#'
BUILD_palinear_TRUE=''
BUILD_palogist_FALSE='#'
BUILD_palogist_TRUE=''
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPPFLAGS='-Wall'
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2 -D_NOT_R_FILEVECTOR'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
HAVE_PDFLATEX_FALSE=''
HAVE_PDFLATEX_TRUE='#'
HAVE_R_FALSE='#'
HAVE_R_TRUE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LN_S='ln -s'
LTLIBOBJS=''
MAINT=''
MAINTAINER_MODE_FALSE='#'
MAINTAINER_MODE_TRUE=''
MAKEINFO='${SHELL} /usr/local/apps/probabel/0.4.2/missing makeinfo'
MKDIR_P='/bin/mkdir -p'
OBJEXT='o'
PACKAGE='probabel'
PACKAGE_BUGREPORT='genabel-devel at r-forge.wu-wien.ac.at'
PACKAGE_NAME='ProbABEL'
PACKAGE_STRING='ProbABEL 0.4.2'
PACKAGE_TARNAME='probabel'
PACKAGE_URL=''
PACKAGE_VERSION='0.4.2'
PATH_SEPARATOR=':'
PDFLATEX=''
R='R'
SED='/usr/local/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
VERSION='0.4.2'
WITH_EIGEN_FALSE=''
WITH_EIGEN_TRUE='#'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /usr/local/apps/probabel/0.4.2/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local/apps/probabel/0.4.2'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "ProbABEL"
#define PACKAGE_TARNAME "probabel"
#define PACKAGE_VERSION "0.4.2"
#define PACKAGE_STRING "ProbABEL 0.4.2"
#define PACKAGE_BUGREPORT "genabel-devel at r-forge.wu-wien.ac.at"
#define PACKAGE_URL ""
#define PACKAGE "probabel"
#define VERSION "0.4.2"
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_ALLOCA_H 1
#define HAVE_ALLOCA 1
#define HAVE_FLOAT_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_LIBINTL_H 1
#define HAVE_LIMITS_H 1
#define HAVE_STDDEF_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_PARAM_H 1
#define HAVE_WCHAR_H 1
#define HAVE_WCTYPE_H 1
#define HAVE_STDBOOL_H 1
#define HAVE_POW 1
#define HAVE_PUTENV 1
#define HAVE_SQRT 1
#define HAVE_STRDUP 1
#define HAVE_STRNCASECMP 1
#define HAVE_FLOOR 1
#define HAVE_FSEEKO 1
configure: exit 0
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