[package - 140arm64-default][biology/gcta] Failed for gcta-1.94.1_1 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sun, 05 May 2024 15:27:25 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/ampere3/data/140arm64-default/9476d3e04f44/logs/gcta-1.94.1_1.log
Build URL:      https://pkg-status.freebsd.org/ampere3/build.html?mastername=140arm64-default&build=9476d3e04f44
Log:

=>> Building biology/gcta
build started at Sun May  5 15:24:40 UTC 2024
port directory: /usr/ports/biology/gcta
package name: gcta-1.94.1_1
building for: FreeBSD 140arm64-default-job-12 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 arm64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 1581 Dec 14 01:07 /usr/ports/biology/gcta/Makefile
Ports top last git commit: 9476d3e04f4
Ports top unclean checkout: no
Port dir last git commit: 22df0dbcfa8
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1400097
Job Id: 12

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=======================<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-1.21.2.pkg
[140arm64-default-job-12] Installing pkg-1.21.2...
[140arm64-default-job-12] Extracting pkg-1.21.2: .......... 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
[140arm64-default-job-12] Installing boost-libs-1.84.0...
[140arm64-default-job-12] `-- Installing icu-74.2_1,1...
[140arm64-default-job-12] `-- Extracting icu-74.2_1,1: .......... done
[140arm64-default-job-12] 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
[140arm64-default-job-12] Installing spectra-1.0.1_1...
[140arm64-default-job-12] `-- Installing eigen-3.4.0_3...
[140arm64-default-job-12] |   `-- Installing blas-3.12.0_1...
[140arm64-default-job-12] |   | `-- Installing gcc13-13.2.0_4...
[140arm64-default-job-12] |   |   `-- Installing binutils-2.40_5,1...
[140arm64-default-job-12] |   |   | `-- 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