diff options
| -rw-r--r-- | INSTALL.md | 2 | ||||
| -rw-r--r-- | RELEASE-NOTES.md | 6 | ||||
| -rw-r--r-- | src/version.h | 6 | ||||
| -rwxr-xr-x | test/dev_test_suite.sh | 10 | ||||
| -rwxr-xr-x | test/test_suite.sh | 14 |
5 files changed, 22 insertions, 16 deletions
@@ -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/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/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 |