[package - 132arm64-quarterly][biology/gcta] Failed for gcta-1.94.1_1 in build
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Date: Sat, 25 May 2024 07:36:03 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/ampere1/data/132arm64-quarterly/39da018952c2/logs/gcta-1.94.1_1.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=132arm64-quarterly&build=39da018952c2
Log:
=>> Building biology/gcta
build started at Sat May 25 07:33:19 UTC 2024
port directory: /usr/ports/biology/gcta
package name: gcta-1.94.1_1
building for: FreeBSD 132arm64-quarterly-job-01 13.2-RELEASE-p11 FreeBSD 13.2-RELEASE-p11 arm64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Apr 14 01:02 /usr/ports/biology/gcta/Makefile
Ports top last git commit: 39da01895
Ports top unclean checkout: no
Port dir last git commit: 1b931669d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1302001
Job Id: 01
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--MAINTAINER--
jwb@FreeBSD.org
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EIGEN3_INCLUDE_DIR=/usr/local/include/eigen3 BOOST_INCLUDE_DIR=/usr/local/include/boost OPENBLAS=/usr/local SPECTRA_INCLUDE_DIR=/usr/local/include/Spectra XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
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socket buffer size (bytes, -b) unlimited
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kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gcta-1.94.1_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[132arm64-quarterly-job-01] Installing pkg-1.21.3...
[132arm64-quarterly-job-01] Extracting pkg-1.21.3: .......... done
===> gcta-1.94.1_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gcta-1.94.1_1
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.94.1_1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.94.1_1 for building
=> SHA256 Checksum OK for jianyangqt-gcta-v1.94.1_GH0.tar.gz.
=> SHA256 Checksum OK for zhilizheng-plink-ng-3744540_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.94.1_1 for building
===> Extracting for gcta-1.94.1_1
=> SHA256 Checksum OK for jianyangqt-gcta-v1.94.1_GH0.tar.gz.
=> SHA256 Checksum OK for zhilizheng-plink-ng-3744540_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for gcta-1.94.1_1
===> Applying FreeBSD patches for gcta-1.94.1_1 from /usr/ports/biology/gcta/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gcta-1.94.1_1 depends on package: boost-libs>0 - not found
===> Installing existing package /packages/All/boost-libs-1.84.0.pkg
[132arm64-quarterly-job-01] Installing boost-libs-1.84.0...
[132arm64-quarterly-job-01] `-- Installing icu-74.2_1,1...
[132arm64-quarterly-job-01] `-- Extracting icu-74.2_1,1: .......... done
[132arm64-quarterly-job-01] Extracting boost-libs-1.84.0: .......... done
=====
Message from boost-libs-1.84.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> gcta-1.94.1_1 depends on package: boost-libs>0 - found
===> Returning to build of gcta-1.94.1_1
===> gcta-1.94.1_1 depends on package: spectra>0 - not found
===> Installing existing package /packages/All/spectra-1.0.1_1.pkg
[132arm64-quarterly-job-01] Installing spectra-1.0.1_1...
[132arm64-quarterly-job-01] `-- Installing eigen-3.4.0_3...
[132arm64-quarterly-job-01] | `-- Installing blas-3.12.0_1...
[132arm64-quarterly-job-01] | | `-- Installing gcc13-13.2.0_4...
[132arm64-quarterly-job-01] | | `-- Installing binutils-2.40_5,1...
[132arm64-quarterly-job-01] | | | `-- Installing gettext-runtime-0.22.5...
<snip>
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:54:25: error: 'uint64_t' has not been declared
54 | void getMaskBitMale(uint64_t *maskp);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:55:5: error: 'uint32_t' does not name a type
55 | uint32_t getSeed();
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:55:5: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:12: error: 'uint32_t' was not declared in this scope
57 | vector<uint32_t>& getSexValidRawIndex();
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:20: error: template argument 1 is invalid
57 | vector<uint32_t>& getSexValidRawIndex();
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:57:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:12: error: 'uint32_t' was not declared in this scope
58 | vector<uint32_t>& getMaleRawIndex();
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:20: error: template argument 1 is invalid
58 | vector<uint32_t>& getMaleRawIndex();
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:58:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:12: error: 'uint32_t' was not declared in this scope
59 | vector<uint32_t>& getMaleExtractIndex();
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:20: error: template argument 1 is invalid
59 | vector<uint32_t>& getMaleExtractIndex();
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:59:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:12: error: 'int8_t' was not declared in this scope
71 | vector<int8_t> sex;
| ^~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:12: note: 'int8_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:18: error: template argument 1 is invalid
71 | vector<int8_t> sex;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:71:18: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:12: error: 'uint32_t' was not declared in this scope
73 | vector<uint32_t> index_keep;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:20: error: template argument 1 is invalid
73 | vector<uint32_t> index_keep;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:73:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:12: error: 'uint32_t' was not declared in this scope
74 | vector<uint32_t> index_rm;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:20: error: template argument 1 is invalid
74 | vector<uint32_t> index_rm;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:74:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:12: error: 'uint32_t' was not declared in this scope
76 | vector<uint32_t> index_keep_sex;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:20: error: template argument 1 is invalid
76 | vector<uint32_t> index_keep_sex;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:76:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:12: error: 'uint32_t' was not declared in this scope
77 | vector<uint32_t> index_keep_male;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:20: error: template argument 1 is invalid
77 | vector<uint32_t> index_keep_male;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:77:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:12: error: 'uint32_t' was not declared in this scope
78 | vector<uint32_t> index_keep_male_extract; // in the sex valid
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:20: error: template argument 1 is invalid
78 | vector<uint32_t> index_keep_male_extract; // in the sex valid
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:78:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:12: error: 'uint8_t' was not declared in this scope
81 | vector<uint8_t> mask_rm;
| ^~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:12: note: 'uint8_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:19: error: template argument 1 is invalid
81 | vector<uint8_t> mask_rm;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:81:19: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:12: error: 'uint32_t' was not declared in this scope
99 | vector<uint32_t> keep_block_index;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:12: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:20: error: template argument 1 is invalid
99 | vector<uint32_t> keep_block_index;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:99:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:12: error: 'uint64_t' was not declared in this scope
100 | vector<uint64_t> mask_items;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:12: note: 'uint64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:20: error: template argument 1 is invalid
100 | vector<uint64_t> mask_items;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:100:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:12: error: 'uint64_t' was not declared in this scope
101 | vector<uint64_t> mask_add_items;
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:12: note: 'uint64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:20: error: template argument 1 is invalid
101 | vector<uint64_t> mask_add_items;
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Pheno.h:101:20: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:71: error: 'uint32_t' was not declared in this scope
32 | bool getCommonSampleIndex(const vector<string> &sampleIDs, vector<uint32_t> &keep_index, vector<uint32_t> &covar_index);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:24:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
23 | #include "Pheno.h"
+++ |+#include <cstdint>
24 |
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:79: error: template argument 1 is invalid
32 | bool getCommonSampleIndex(const vector<string> &sampleIDs, vector<uint32_t> &keep_index, vector<uint32_t> &covar_index);
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:79: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:101: error: 'uint32_t' was not declared in this scope
32 | bool getCommonSampleIndex(const vector<string> &sampleIDs, vector<uint32_t> &keep_index, vector<uint32_t> &covar_index);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:101: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:109: error: template argument 1 is invalid
32 | bool getCommonSampleIndex(const vector<string> &sampleIDs, vector<uint32_t> &keep_index, vector<uint32_t> &covar_index);
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:109: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:82: error: 'uint32_t' was not declared in this scope
34 | bool getCovarXRaw(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:82: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:90: error: template argument 1 is invalid
34 | bool getCovarXRaw(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:90: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:79: error: 'uint32_t' was not declared in this scope
35 | bool getCovarX(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:79: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:87: error: template argument 1 is invalid
35 | bool getCovarX(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ^
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:87: error: template argument 2 is invalid
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:333:6: error: no declaration matches 'bool Covar::getCommonSampleIndex(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<unsigned int>&, std::vector<unsigned int>&)'
333 | bool Covar::getCommonSampleIndex(const vector<string> &sampleIDs, vector<uint32_t> &keep_index, vector<uint32_t> &covar_index){
| ^~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:32:10: note: candidate is: 'bool Covar::getCommonSampleIndex(const std::vector<std::__cxx11::basic_string<char> >&, int&, int&)'
32 | bool getCommonSampleIndex(const vector<string> &sampleIDs, vector<uint32_t> &keep_index, vector<uint32_t> &covar_index);
| ^~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:29:7: note: 'class Covar' defined here
29 | class Covar{
| ^~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:354:6: error: no declaration matches 'bool Covar::getCovarX(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double>&, std::vector<unsigned int>&)'
354 | bool Covar::getCovarX(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index){
| ^~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:10: note: candidate is: 'bool Covar::getCovarX(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double>&, int&)'
35 | bool getCovarX(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ^~~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:29:7: note: 'class Covar' defined here
29 | class Covar{
| ^~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:420:6: error: no declaration matches 'bool Covar::getCovarXRaw(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double>&, std::vector<unsigned int>&)'
420 | bool Covar::getCovarXRaw(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index){
| ^~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:10: note: candidate is: 'bool Covar::getCovarXRaw(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double>&, int&)'
34 | bool getCovarXRaw(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ^~~~~~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:29:7: note: 'class Covar' defined here
29 | class Covar{
| ^~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp: In static member function 'static int Covar::registerOption(std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&)':
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:616:40: error: cannot convert 'std::vector<unsigned int>' to 'int&'
616 | covar.getCovarXRaw(samples, X, sample_index);
| ^~~~~~~~~~~~
| |
| std::vector<unsigned int>
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:34:93: note: initializing argument 3 of 'bool Covar::getCovarXRaw(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double>&, int&)'
34 | bool getCovarXRaw(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:627:37: error: cannot convert 'std::vector<unsigned int>' to 'int&'
627 | covar.getCovarX(samples, X, sample_index);
| ^~~~~~~~~~~~
| |
| std::vector<unsigned int>
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/Covar.h:35:90: note: initializing argument 3 of 'bool Covar::getCovarX(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double>&, int&)'
35 | bool getCovarX(const vector<string> &sampleIDs, vector<double> &X, vector<uint32_t> &keep_index);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~
[ 2% 3/67] /usr/local/bin/g++13 -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/grm.dir/src/GRM.cpp.o -MF CMakeFiles/grm.dir/src/GRM.cpp.o.d -o CMakeFiles/grm.dir/src/GRM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp
[ 4% 3/67] /usr/local/bin/g++13 -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -MF CMakeFiles/fastfam.dir/src/FastFAM.cpp.o.d -o CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp
ninja: build stopped: subcommand failed.
===> 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