[package - 132amd64-default][biology/gcta] Failed for gcta-1.26.0_4 in build
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Date: Sun, 08 Oct 2023 04:25:06 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy16/data/132amd64-default/ecb3f8a4918b/logs/gcta-1.26.0_4.log
Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=132amd64-default&build=ecb3f8a4918b
Log:
=>> Building biology/gcta
build started at Sun Oct 8 04:23:06 UTC 2023
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_4
building for: FreeBSD 132amd64-default-job-06 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 amd64
maintained by: jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.7.pkg
[132amd64-default-job-06] Installing pkg-1.20.7...
[132amd64-default-job-06] Extracting pkg-1.20.7: .......... done
===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_4 for building
=> SHA256 Checksum OK for gcta_1.26.0_src.zip.
=> SHA256 Checksum OK for eigen-3.3.9.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_4 for building
===> Extracting for gcta-1.26.0_4
=> SHA256 Checksum OK for gcta_1.26.0_src.zip.
=> SHA256 Checksum OK for eigen-3.3.9.tar.gz.
Archive: /portdistfiles/gcta_1.26.0_src.zip
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/bivar_reml.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/cdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Copyright.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/data.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/edata.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ejma.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/est_hsq.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gcta.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/GNU_General_Public_License_v3.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/grm.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gwas_simu.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/HowToCompile.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ipmpar.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/joint_meta.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ld.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Makefile
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mkl.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mlm_assoc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/option.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/popu_genet.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/raw_geno.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/read_imput.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/README.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/reml_within_family.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/sbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/UnusedCode.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.h
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for gcta-1.26.0_4
===> Converting DOS text files to UNIX text files
===> Applying FreeBSD patches for gcta-1.26.0_4 from /usr/ports/biology/gcta/files
===========================================================================
=======================<phase: build-depends >============================
===> gcta-1.26.0_4 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[132amd64-default-job-06] Installing gmake-4.3_2...
[132amd64-default-job-06] `-- Installing gettext-runtime-0.22_1...
[132amd64-default-job-06] | `-- Installing indexinfo-0.3.1...
[132amd64-default-job-06] | `-- Extracting indexinfo-0.3.1: .... done
[132amd64-default-job-06] `-- Extracting gettext-runtime-0.22_1: .......... done
[132amd64-default-job-06] Extracting gmake-4.3_2: .......... done
===> gcta-1.26.0_4 depends on package: gmake>=4.3 - found
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: lib-depends >============================
===> gcta-1.26.0_4 depends on shared library: libopenblas.so - not found
===> Installing existing package /packages/All/openblas-0.3.24,1.pkg
[132amd64-default-job-06] Installing openblas-0.3.24,1...
[132amd64-default-job-06] `-- Installing gcc12-12.2.0_6...
[132amd64-default-job-06] | `-- Installing binutils-2.40_4,1...
[132amd64-default-job-06] | | `-- Installing zstd-1.5.5...
[132amd64-default-job-06] | | `-- Installing liblz4-1.9.4,1...
[132amd64-default-job-06] | | `-- Extracting liblz4-1.9.4,1: .......... done
[132amd64-default-job-06] | | `-- Extracting zstd-1.5.5: .......... done
[132amd64-default-job-06] | `-- Extracting binutils-2.40_4,1: .......... done
[132amd64-default-job-06] | `-- Installing gmp-6.3.0...
[132amd64-default-job-06] | `-- Extracting gmp-6.3.0: .......... done
[132amd64-default-job-06] | `-- Installing mpc-1.3.1_1...
[132amd64-default-job-06] | | `-- Installing mpfr-4.2.1,1...
[132amd64-default-job-06] | | `-- Extracting mpfr-4.2.1,1: .......... done
[132amd64-default-job-06] | `-- Extracting mpc-1.3.1_1: ......... done
[132amd64-default-job-06] `-- Extracting gcc12-12.2.0_6: .......... done
[132amd64-default-job-06] Extracting openblas-0.3.24,1: .......... done
=====
Message from gcc12-12.2.0_6:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> gcta-1.26.0_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: configure >============================
===> Configuring for gcta-1.26.0_4
===========================================================================
=======================<phase: build >============================
===> Building for gcta-1.26.0_4
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0'
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c bivar_reml.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c CommFunc.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c eigen_func.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c data.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c dcdflib.cpp
dcdflib.cpp:6027:23: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
if(qcond) ftnstop(" SMALL, X, BIG not monotone in INVR");
^
dcdflib.cpp:6403:28: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
if(xx < 5.0e0) ftnstop(" Argument too small in DLANOR");
^
dcdflib.cpp:6784:29: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
if(*z <= 0.0e0) ftnstop("Zero or negative argument in DSTREM");
^
bivar_reml.cpp:321:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c edata.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c ejma.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c est_hsq.cpp
est_hsq.cpp:893:25: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."};
^
est_hsq.cpp:893:46: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."};
^
est_hsq.cpp:893:68: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
char *mtd_str[3] = {"AI-REML algorithm", "Fisher-scoring ...", "EM-REML algorithm ..."};
^
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c grm.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c gwas_simu.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c ld.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c joint_meta.cpp
joint_meta.cpp:179:34: warning: implicit conversion of out of range value from 'double' to 'int' is undefined [-Wliteral-conversion]
if (top_SNPs < 0) top_SNPs = 1e30;
~ ^~~~
joint_meta.cpp:218:24: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if (!joint_only && !mld_slct_alg==2) {
^ ~~
joint_meta.cpp:218:24: note: add parentheses after the '!' to evaluate the comparison first
if (!joint_only && !mld_slct_alg==2) {
^
( )
joint_meta.cpp:218:24: note: add parentheses around left hand side expression to silence this warning
if (!joint_only && !mld_slct_alg==2) {
^
( )
joint_meta.cpp:218:37: warning: result of comparison of constant 2 with expression of type 'bool' is always false [-Wtautological-constant-out-of-range-compare]
if (!joint_only && !mld_slct_alg==2) {
~~~~~~~~~~~~~^ ~
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c mlm_assoc.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c mkl.cpp
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c option.cpp
option.cpp:135:24: warning: ISO C++11 does not allow conversion from string literal to 'std::vector<char *>::value_type' (aka 'char *') [-Wwritable-strings]
argv[option_num] = "gcta";
^
option.cpp:136:28: warning: ISO C++11 does not allow conversion from string literal to 'std::vector<char *>::value_type' (aka 'char *') [-Wwritable-strings]
argv[option_num + 1] = "gcta";
^
mkl.cpp:360:5: error: no matching function for call to 'dpotrf_'
dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info);
^~~~~~~
/usr/local/include/lapack.h:13624:12: note: candidate function not viable: requires 6 arguments, but 5 were provided
lapack_int LAPACK_dpotrf_base(
^
/usr/local/include/lapack.h:13623:28: note: expanded from macro 'LAPACK_dpotrf_base'
#define LAPACK_dpotrf_base LAPACK_GLOBAL(dpotrf,DPOTRF)
^
/usr/local/include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
^
<scratch space>:36:1: note: expanded from here
dpotrf_
^
mkl.cpp:372:9: error: no matching function for call to 'dpotri_'
dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info);
^~~~~~~
/usr/local/include/lapack.h:13752:6: note: candidate function not viable: requires 6 arguments, but 5 were provided
void LAPACK_dpotri_base(
^
/usr/local/include/lapack.h:13751:28: note: expanded from macro 'LAPACK_dpotri_base'
#define LAPACK_dpotri_base LAPACK_GLOBAL(dpotri,DPOTRI)
^
/usr/local/include/lapacke_mangling.h:12:39: note: expanded from macro 'LAPACK_GLOBAL'
#define LAPACK_GLOBAL(lcname,UCNAME) lcname##_
^
<scratch space>:44:1: note: expanded from here
dpotri_
^
2 errors generated.
gmake[1]: *** [Makefile:72: mkl.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
2 warnings generated.
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/gcta