[med-svn] [Git][med-team/plink2][master] 5 commits: Add some debug code
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Feb 18 12:03:53 GMT 2022
Andreas Tille pushed to branch master at Debian Med / plink2
Commits:
4369d4ba by Andreas Tille at 2022-02-18T11:45:57+01:00
Add some debug code
- - - - -
8ee51a44 by Andreas Tille at 2022-02-18T12:14:33+01:00
Drop debug code
- - - - -
455de02d by Andreas Tille at 2022-02-18T12:15:15+01:00
Normalise name of autopkgtest script
- - - - -
f4d55d33 by Andreas Tille at 2022-02-18T12:16:59+01:00
Add some debug output
- - - - -
bf51ee93 by Andreas Tille at 2022-02-18T12:35:21+01:00
Fix check
- - - - -
9 changed files:
- + debian/README.test
- debian/bin/simd-dispatch
- debian/changelog
- + debian/docs
- debian/examples
- + debian/patches/debug.patch
- debian/patches/series
- debian/tests/control
- debian/tests/run-sample-analysis → debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/bin/simd-dispatch
=====================================
@@ -28,4 +28,5 @@ test_and_run_avx2 "@"
for SIMD in avx sse4.1 ssse3 sse3 sse2 sse mmx ; do test_and_run ${SIMD} "$@" ; done
# fallback to plain option
+set -x
"$BASE-plain" "$@"
=====================================
debian/changelog
=====================================
@@ -5,6 +5,7 @@ plink2 (2.00~a3-220129+dfsg-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* Standards-Version: 4.6.0 (routine-update)
+ * Add some debug code
TODO: autopkgtest: /usr/bin/plink2: line 8: 156 Segmentation fault "${cmd}" "$@"
-> see bug #1004037
=====================================
debian/docs
=====================================
@@ -0,0 +1,2 @@
+debian/tests/run-unit-test
+debian/README.test
=====================================
debian/examples
=====================================
@@ -3,5 +3,4 @@ debian/upstream.docs/toy.ped
debian/upstream.docs/toy.map
# Expected outputs and script for autopkgtest
-debian/tests/run-sample-analysis
debian/tests/output_tests/*
=====================================
debian/patches/debug.patch
=====================================
@@ -0,0 +1,49 @@
+From 5ee527d39176d5d612014ce39a1e1ecbe59b3d9c Mon Sep 17 00:00:00 2001
+From: Christopher Chang <chrchang523 at gmail.com>
+Date: Thu, 17 Feb 2022 19:08:02 -0800
+Subject: [PATCH] add terminal --debug prints
+Origin: https://github.com/chrchang/plink-ng/commit/5ee527d39176d5d612014ce39a1e1ecbe59b3d9c.patch
+
+---
+ 2.0/plink2.cc | 6 ++++++
+ 2.0/plink2_cmdline.cc | 6 ++++++
+ 2 files changed, 12 insertions(+)
+
+diff --git a/plink2.cc b/2.0/plink2.cc
+index c9ed51a5..83b28814 100644
+--- a/plink2.cc
++++ b/plink2.cc
+@@ -10944,7 +10944,13 @@ int main(int argc, char** argv) {
+ reterr = kPglRetWriteFail;
+ }
+ if (bigstack_ua) {
++ if (g_debug_on) {
++ fputs("--debug: Trying to free bigstack_ua.\n", stdout);
++ }
+ free(bigstack_ua);
+ }
++ if (g_debug_on) {
++ fputs("--debug: Exiting.\n", stdout);
++ }
+ return S_CAST(int32_t, reterr);
+ }
+diff --git a/plink2_cmdline.cc b/2.0/plink2_cmdline.cc
+index 4c49ccee..b02aace5 100644
+--- a/plink2_cmdline.cc
++++ b/plink2_cmdline.cc
+@@ -526,9 +526,15 @@ BoolErr CleanupLogfile(uint32_t print_end_time) {
+ }
+ BoolErr ret_boolerr = 0;
+ if (g_logfile) {
++ if (g_debug_on) {
++ printf("--debug: g_log_failed = %u.\n", g_log_failed);
++ }
+ if (!g_log_failed) {
+ logputs_silent("\n");
+ logputs_silent(g_logbuf);
++ if (g_debug_on) {
++ fputs("--debug: Trying to close log.\n", stdout);
++ }
+ if (unlikely(fclose(g_logfile))) {
+ fflush(stdout);
+ fprintf(stderr, "Error: Failed to finish writing to log: %s.\n", strerror(errno));
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
Fix_Makefile.patch
use_packaged_libdeflate.patch
baseline
+debug.patch
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: run-sample-analysis
+Tests: run-unit-test
Depends: @
Restrictions: allow-stderr
=====================================
debian/tests/run-sample-analysis → debian/tests/run-unit-test
=====================================
@@ -4,12 +4,14 @@
pkg=plink2
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
-plink2 --dummy 33 65537 0.1 dosage-freq=0.1 --out tmp_data
-plink2 --pfile tmp_data --export vcf vcf-dosage=DS --out tmp_data2
-plink2 --vcf tmp_data2.vcf dosage=DS --out tmp_data2
-
-rm -f $AUTOPKGTEST_TMP/*
-
+plink2 --debug --dummy 33 65537 0.1 dosage-freq=0.1 --out tmp_data
+if [ ! -e tmp_data.pgen ] ; then
+ echo "plink2 failed to create tmp_data.pgen"
+ exit 1
+fi
+plink2 --debug --pfile tmp_data --export vcf vcf-dosage=DS --out tmp_data2
+plink2 --debug --vcf tmp_data2.vcf dosage=DS --out tmp_data2
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd
--
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/dd1538b33f33e2e4fe4963acf0a6dc3f960c2b3d...bf51ee937473385bc54b5faca553f59e62120fdd
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