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-rw-r--r--INSTALL.md2
-rw-r--r--RELEASE-NOTES.md6
-rw-r--r--src/fastblas.cpp5
-rw-r--r--src/fastblas.h2
-rw-r--r--src/fastopenblas.h9
-rw-r--r--src/gemma.cpp2
-rw-r--r--src/version.h6
-rwxr-xr-xtest/dev_test_suite.sh10
-rw-r--r--test/src/unittests-math.cpp2
-rwxr-xr-xtest/test_suite.sh14
10 files changed, 26 insertions, 32 deletions
diff --git a/INSTALL.md b/INSTALL.md
index 4885ed0..6e5c665 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -54,7 +54,7 @@ To build GEMMA from source you can opt to install the build tools with GNU Guix
The current build container is
- guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim
+ guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim which
### Install from source
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
index a83190b..6dad528 100644
--- a/RELEASE-NOTES.md
+++ b/RELEASE-NOTES.md
@@ -4,6 +4,12 @@ see
and
[commits](https://github.com/genetics-statistics/GEMMA/commits/master).
+## ChangeLog v0.98.2 (2018/05/28)
+
+GCC 10.1 fix release
+
+* Fix build on gcc 10.1 (mostly BLAS include files)
+
## ChangeLog v0.98.1 (2018/12/10)
Bug fix release
diff --git a/src/fastblas.cpp b/src/fastblas.cpp
index 42c59ee..41ee741 100644
--- a/src/fastblas.cpp
+++ b/src/fastblas.cpp
@@ -18,18 +18,13 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
-// #include "gsl/gsl_matrix.h"
#include <algorithm> // std::min
#include <cmath>
#include <iomanip>
#include <vector>
#include "debug.h"
-#include "fastblas.h"
-#include "fastopenblas.h"
#include "mathfunc.h"
#include <string.h>
-#include "eigenlib.h"
-#include <cblas.h>
const char *FastblasTrans = "T";
const char *FastblasNoTrans = "N";
diff --git a/src/fastblas.h b/src/fastblas.h
index cca3258..32253b3 100644
--- a/src/fastblas.h
+++ b/src/fastblas.h
@@ -23,7 +23,7 @@
#include <assert.h>
#include <iostream>
-#include "gsl/gsl_matrix.h"
+// #include "gsl/gsl_matrix.h"
gsl_matrix *fast_copy(gsl_matrix *m, const double *mem);
diff --git a/src/fastopenblas.h b/src/fastopenblas.h
index 7f453da..ace8347 100644
--- a/src/fastopenblas.h
+++ b/src/fastopenblas.h
@@ -21,13 +21,8 @@
#ifndef __FASTOPENBLAS_H__
#define __FASTOPENBLAS_H__
-#include <assert.h>
-#include <iostream>
-extern "C"
-{
- #include <cblas.h> // For OpenBlas / Atlas
-}
-// #include "gsl/gsl_matrix.h"
+// #include <assert.h>
+// #include <iostream>
void fast_cblas_dgemm(const enum CBLAS_ORDER ,
const enum CBLAS_TRANSPOSE TransA,
diff --git a/src/gemma.cpp b/src/gemma.cpp
index 6bc739b..7b955cd 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -28,7 +28,7 @@
#ifdef OPENBLAS
extern "C" {
// these functions are defined in cblas.h - but if we include that we
- // conflicts with other BLAS includes
+ // conflicts with other BLAS includes (GSL)
int openblas_get_num_threads(void);
int openblas_get_parallel(void);
char* openblas_get_config(void);
diff --git a/src/version.h b/src/version.h
index d413933..f97c9f1 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,5 +1,5 @@
-// version.h generated by GEMMA scripts/gen_version_info.sh
+// version.h generated by GEMMA ./scripts/gen_version_info.sh
#define GEMMA_VERSION "0.98.2"
-#define GEMMA_DATE "2020-05-22"
+#define GEMMA_DATE "2020-05-28"
#define GEMMA_YEAR "2020"
-#define GEMMA_PROFILE "/gnu/store/h9xwdvc7kqx7cvpvs6iascfdw5zgzhyd-profile"
+#define GEMMA_PROFILE ""
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 7ea0e57..b10fedd 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -16,7 +16,7 @@ testLinearModel() {
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8_lm.assoc.txt
assertEquals "118459" `wc -w < $outfn`
- assertEquals "4053667109.69" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "4053667109.67" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
# Related to https://github.com/genetics-statistics/GEMMA/issues/78
@@ -46,7 +46,7 @@ testBXDStandardRelatednessMatrixK() {
assertEquals 0 $?
outfn=output/$outn.cXX.txt
assertEquals "198" `wc -l < $outfn`
- assertEquals "-116.11" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "-116.13" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBXDLMLikelihoodRatio() {
@@ -62,7 +62,7 @@ testBXDLMLikelihoodRatio() {
outfn=output/$outn.assoc.txt
assertEquals "95134" `wc -w < $outfn`
- assertEquals "3089042886.28" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "3089042886.08" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBXDLMMLikelihoodRatio() {
@@ -78,7 +78,7 @@ testBXDLMMLikelihoodRatio() {
outfn=output/$outn.assoc.txt
assertEquals "73180" `wc -w < $outfn`
- assertEquals "3088458212.93" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "3088458212.86" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testCenteredRelatednessMatrixissue188() {
@@ -87,7 +87,7 @@ testCenteredRelatednessMatrixissue188() {
$gemma $gemmaopts -b data/issue188/2000 -gk -o $outn
assertEquals 0 $?
outfn=output/$outn.cXX.txt
- assertEquals "193.80" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "193.78" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testLMMissue188() {
diff --git a/test/src/unittests-math.cpp b/test/src/unittests-math.cpp
index d82f656..4872e9a 100644
--- a/test/src/unittests-math.cpp
+++ b/test/src/unittests-math.cpp
@@ -1,8 +1,6 @@
#include <catch.hpp>
#include <iostream>
#include <fenv.h>
-#include "gsl/gsl_matrix.h"
-// #include <cblas.h>
#include <algorithm>
#include <limits>
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 0162d08..cea8a22 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -26,7 +26,7 @@ testBslmm2() {
-gk 1 -o $outn
assertEquals 0 $?
outfn=output/$outn.cXX.txt
- assertEquals "579.66" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "579.50" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testBslmm3() {
@@ -87,7 +87,7 @@ testCenteredRelatednessMatrixKFullLOCO1() {
assertEquals 0 $?
outfn=output/$outn.cXX.txt
assertEquals "1940" `wc -l < $outfn`
- assertEquals "2246.57" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "2246.49" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testUnivariateLinearMixedModelFullLOCO1() {
@@ -105,7 +105,7 @@ testUnivariateLinearMixedModelFullLOCO1() {
assertEquals 0 $?
outfn=output/$outn.assoc.txt
assertEquals "951" `wc -l < $outfn`
- assertEquals "267507851.98" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "267507852.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testCenteredRelatednessMatrixK() {
@@ -117,7 +117,7 @@ testCenteredRelatednessMatrixK() {
assertEquals "1940" `wc -l < $outfn`
assertEquals "3763600" `wc -w < $outfn`
assertEquals "0.335" `head -c 5 $outfn`
- assertEquals "1119.64" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "1119.60" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testUnivariateLinearMixedModel() {
@@ -133,7 +133,7 @@ testUnivariateLinearMixedModel() {
assertEquals 0 $?
outfn=output/mouse_hs1940_CD8_lmm.assoc.txt
assertEquals "129228" `wc -w < $outfn`
- assertEquals "4038540440.86" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "4038540440.81" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testLinearMixedModelPhenotypes() {
@@ -148,7 +148,7 @@ testLinearMixedModelPhenotypes() {
outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
assertEquals "139867" `wc -w < $outfn`
- assertEquals "4029037056.54" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "4029037056.58" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
testPlinkStandardRelatednessMatrixK() {
@@ -160,7 +160,7 @@ testPlinkStandardRelatednessMatrixK() {
-gk 2 -o $testname
assertEquals 0 $?
assertEquals "427" `wc -l < $outfn`
- assertEquals "-358.07" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+ assertEquals "-358.05" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}
# Test for https://github.com/genetics-statistics/GEMMA/issues/58
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 06:12:16 +0000