From 928eed79ff815d782d663f98c614c6cf87eb858b Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Wed, 11 Jun 2025 18:10:50 -0700 Subject: [PATCH 1/3] src/abismal: updating submodule --- src/abismal | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/abismal b/src/abismal index 3e53fe26..4a99721a 160000 --- a/src/abismal +++ b/src/abismal @@ -1 +1 @@ -Subproject commit 3e53fe269177c38a9be6797157b3454c0a46fa46 +Subproject commit 4a99721adc5ed43e3d6254e6e126727b4b4c4496 From ffad2b39801394726818c4bf34e1db2b57dc5c67 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Wed, 11 Jun 2025 18:15:09 -0700 Subject: [PATCH 2/3] configure.ac: updates for better library dependency checking --- configure.ac | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/configure.ac b/configure.ac index 057daec9..512e1704 100644 --- a/configure.ac +++ b/configure.ac @@ -1,6 +1,6 @@ dnl This file is part of dnmtools dnl -dnl Copyright (C) 2022-2024: Andrew D. Smith +dnl Copyright (C) 2022-2025: Andrew D. Smith dnl dnl Authors: Andrew D. Smith dnl @@ -32,19 +32,21 @@ AC_CONFIG_SUBDIRS([src/smithlab_cpp]) dnl check for HTSLib if requested hts_fail_msg=" -Failed to locate HTSLib on your system. Please use the LDFLAGS and -CPPFLAGS variables to specify the directories where the HTSLib library -and headers can be found. +Failed to locate HTSLib on your system. Please use the LDFLAGS and CPPFLAGS +variables to specify the directories where the HTSLib library and headers can +be found. " gsl_fail_msg=" -Failed to locate the GNU Scientific Library (GSL) on your -system. Please use the LDFLAGS and CPPFLAGS variables to specify the -directories where the GSL library and headers can be found. +Failed to locate the GNU Scientific Library (GSL) on your system. Please use +the LDFLAGS and CPPFLAGS variables to specify the directories where the GSL +library and headers can be found. " dnl check for required libraries -AC_SEARCH_LIBS([hts_version], [hts], [], [AC_MSG_FAILURE([$hts_fail_msg])]) +AC_SEARCH_LIBS([pthread_create], [pthread], [], [AC_MSG_FAILURE(["pthread library not found"])]) +AC_SEARCH_LIBS([gzopen], [z], [], [AC_MSG_FAILURE(["Zlib library not found"])]) +AC_SEARCH_LIBS([hts_version], [hts], [], [AC_MSG_FAILURE([$hts_fail_msg])], [-lz -lpthread]) AC_SEARCH_LIBS([cblas_dgemm], [gslcblas], [], [AC_MSG_FAILURE([$gsl_fail_msg])]) AC_SEARCH_LIBS([gsl_blas_dgemm], [gsl], [], [AC_MSG_FAILURE([$gsl_fail_msg])]) From 668e46648323bf0702a71a8679a73d87aa92167d Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 13:46:06 -0700 Subject: [PATCH 3/3] src/abismal: updating submodule --- src/abismal | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/abismal b/src/abismal index 4a99721a..83a59a6a 160000 --- a/src/abismal +++ b/src/abismal @@ -1 +1 @@ -Subproject commit 4a99721adc5ed43e3d6254e6e126727b4b4c4496 +Subproject commit 83a59a6ade2013d579ea175014aea0ef52f2a4e4