[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_24 #13358
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Sun Dec 25 11:59:11 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_armhf_24/13358/------------------------------------------
[...truncated 7129 lines...]
source/commands/chimerauchimecommand.cpp:1501:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
@@ -1505,73 +1509,81 @@
return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
^
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp
-source/commands/clustersplitcommand.cpp: In member function 'int ClusterSplitCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double)':
-source/commands/clustersplitcommand.cpp:1485:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
- system(commandString.c_str());
- ^
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
source/commands/pairwiseseqscommand.cpp:342:46: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(("gzip -v " + outputFile).c_str());
^
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp
+source/commands/clustersplitcommand.cpp: In member function 'int ClusterSplitCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double)':
+source/commands/clustersplitcommand.cpp:1485:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
+ system(commandString.c_str());
+ ^
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp
+source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
+source/commands/clustercommand.cpp:567:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
+ system(commandString.c_str());
+ ^
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/database.o source/datastructures/database.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::__cxx11::string, std::__cxx11::string)':
source/datastructures/blastalign.cpp:63:30: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as
^
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/database.o source/datastructures/database.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedsabundvector.o source/datastructures/sharedsabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int)':
source/datastructures/blastdb.cpp:230:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str());
@@ -1584,16 +1596,18 @@
source/datastructures/blastdb.cpp:366:34: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
^
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/forest.o source/randomforest/forest.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp
@@ -1609,18 +1623,10 @@
system(command.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp
+g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatphylip.o source/read/formatphylip.cpp
-source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
-source/read/formatphylip.cpp:108:29: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
- system(command.c_str());
- ^
-source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)':
-source/read/formatphylip.cpp:338:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
- system(command.c_str());
- ^
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp
-g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp
g++ -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"8/9/2016\"" -DVERSION="\"1.38.1\"" -O3 -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp
cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
@@ -1638,6 +1644,14 @@
+ echo alignchime
alignchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/mothur-1.38.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"8/9/2016\""' '-DVERSION="\"1.38.1\""' -O3 -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchime.cpp -o alignchime.o
+source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
+source/read/formatphylip.cpp:108:29: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
+ system(command.c_str());
+ ^
+source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)':
+source/read/formatphylip.cpp:338:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
+ system(command.c_str());
+ ^
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
@@ -1787,10 +1801,10 @@
+ cat tmp.stderr
+ rm -f tmp.stderr
+ ls -lh uchime
--rwxr-xr-x 1 pbuilder1 pbuilder1 2.3M Dec 24 21:56 uchime
+-rwxrwxr-x 1 pbuilder2 pbuilder2 2.3M Dec 26 01:17 uchime
+ sum uchime
06336 2345
-g++ -Wl,-z,relro -Wl,-z,now -L "\"Enter_your_boost_library_path_here\"" -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/gotohoverlap.o source/validparameter.o source/heatmap.o source/nast.o source/randomnumber.o source/mothurout.o source/completelinkage.o source/averagelinkage.o source/collect.o source/seqnoise.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/vsearchfileparser.o source/weightedlinkage.o source/refchimeratest.o source/slibshuff.o source/trialSwap2.o source/sharedutilities.o source/consensus.o source/fileoutput.o source/cluster.o source/nastreport.o source/needlemanoverlap.o source/myseqdist.o source/subsample.o source/commandfactory.o source/rarecalc.o source/rarefact.o source/wilcox.o source/progress.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/mothur.o source/engine.o source/linearalgebra.o source/dlibshuff.o source/heatmapsim.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/noalign.o source/overlap.o source/calculators/calculator.o source/calculators/sharedthetayc.o source/calculators/coverage.o source/calculators/sharedmorisitahorn.o source/calculators/sharedace.o source/calculators/qstat.o source/calculators/bergerparker.o source/calculators/sharedsobs.o source/calculators/parsimony.o source/calculators/shen.o source/calculators/canberra.o source/calculators/gower.o source/calculators/smithwilson.o source/calculators/structeuclidean.o source/calculators/simpson.o source/calculators/mempearson.o source/calculators/logsd.o source/calculators/sharedkulczynskicody.o source/calculators/memchord.o source/calculators/manhattan.o source/calculators/geom.o source/calculators/jackknife.o source/calculators/whittaker.o source/calculators/efron.o source/calculators/bootstrap.o source/calculators/hamming.o source/calculators/sharedkstest.o source/calculators/sharedjackknife.o source/calculators/invsimpson.o source/calculators/sharedsorclass.o source/calculators/prng.o source/calculators/npshannon.o source/calculators/sharedrjsd.o source/calculators/sharedochiai.o source/calculators/sharedchao1.o source/calculators/unweighted.o source/calculators/chao1.o source/calculators/simpsoneven.o source/calculators/memchi2.o source/calculators/shannon.o source/calculators/structkulczynski.o source/calculators/spearman.o source/calculators/structchord.o source/calculators/shannoneven.o source/calculators/bstick.o source/calculators/solow.o source/calculators/sharedjsd.o source/calculators/sharedjest.o source/calculators/sharedsobscollectsummary.o source/calculators/sharedanderbergs.o source/calculators/goodscoverage.o source/calculators/odum.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedlennon.o source/calculators/memeuclidean.o source/calculators/sharedjabund.o source/calculators/boneh.o source/calculators/uvest.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedjclass.o source/calculators/shannonrange.o source/calculators/sharedmarczewski.o source/calculators/sharedsorabund.o source/calculators/sharedkulczynski.o source/calculators/weighted.o source/calculators/sharedbraycurtis.o source/calculators/hellinger.o source/calculators/sharedthetan.o source/calculators/structchi2.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/chimerarealigner.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/cmdargs.o source/clearcut/getopt_long.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/commands/collectcommand.o source/commands/chimeraccodecommand.o source/commands/getcommandinfocommand.o source/commands/getotuscommand.o source/commands/distancecommand.o source/commands/listseqscommand.o source/commands/clusterdoturcommand.o source/commands/heatmapcommand.o source/commands/quitcommand.o source/commands/removegroupscommand.o source/commands/indicatorcommand.o source/commands/getlineagecommand.o source/commands/libshuffcommand.o source/commands/clusterfragmentscommand.o source/commands/treegroupscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/venncommand.o source/commands/renameseqscommand.o source/commands/setseedcommand.o source/commands/makegroupcommand.o source/commands/getcoremicrobiomecommand.o source/commands/classifyseqscommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/removerarecommand.o source/commands/unifracweightedcommand.o source/commands/createdatabasecommand.o source/commands/splitgroupscommand.o source/commands/sffmultiplecommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/seqerrorcommand.o source/commands/aligncommand.o source/commands/getgroupscommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/chimerabellerophoncommand.o source/commands/getsharedotucommand.o source/commands/parsefastaqcommand.o source/commands/rarefactcommand.o source/commands/removeotulabelscommand.o source/commands/screenseqscommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/homovacommand.o source/commands/anosimcommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getlistcountcommand.o source/commands/catchallcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/matrixoutputcommand.o source/commands/makecontigscommand.o source/commands/makelookupcommand.o source/commands/summarysharedcommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/trimseqscommand.o source/commands/consensusseqscommand.o source/commands/listotulabelscommand.o source/commands/mimarksattributescommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/phylodiversitycommand.o source/commands/filtersharedcommand.o source/commands/shhhercommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/seqsummarycommand.o source/commands/pcacommand.o source/commands/makebiomcommand.o source/commands/metastatscommand.o source/commands/subsamplecommand.o source/commands/getrabundcommand.o source/commands/chimeraslayercommand.o source/commands/chopseqscommand.o source/commands/sffinfocommand.o source/commands/getlabelcommand.o source/commands/corraxescommand.o source/commands/cooccurrencecommand.o source/commands/preclustercommand.o source/commands/setdircommand.o source/commands/classifytreecommand.o source/commands/mergetaxsummarycommand.o source/commands/getseqscommand.o source/commands/collectsharedcommand.o source/commands/deuniqueseqscommand.o source/commands/getmimarkspackagecommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/clearcutcommand.o source/commands/sharedcommand.o source/commands/mergefilecommand.o source/commands/pcoacommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/getgroupcommand.o source/commands/makefastqcommand.o source/commands/helpcommand.o source/commands/removeotuscommand.o source/commands/mergegroupscommand.o source/commands/pcrseqscommand.o source/commands/systemcommand.o source/commands/chimeraperseuscommand.o source/commands/deuniquetreecommand.o source/commands/binsequencecommand.o source/commands/makelefsecommand.o source/commands/mgclustercommand.o source/commands/classifyotucommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/removedistscommand.o source/commands/amovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/kruskalwalliscommand.o source/commands/chimeracheckcommand.o source/commands/clustersplitcommand.o source/commands/pairwiseseqscommand.o source/commands/nocommands.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/setlogfilecommand.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/rarefactsharedcommand.o source/commands/newcommandtemplate.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/commands/reversecommand.o source/commands/getcurrentcommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/kmer.o source/datastructures/suffixdb.o source/datastructures/sharedordervector.o source/datastructures/fastamap.o source/datastructures/distancedb.o source/datastructures/sharedlistvector.o source/datastructures/alignmentcell.o source/datastructures/nameassignment.o source/datastructures/fastqread.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/counttable.o source/datastructures/sparsedistancematrix.o source/datastructures/listvector.o source/datastructures/kmeralign.o source/datastructures/sparsematrix.o source/datastructures/alignmentdb.o source/datastructures/fullmatrix.o source/datastructures/blastalign.o source/datastructures/treenode.o source/datastructures/sabundvector.o source/datastructures/rabundvector.o source/datastructures/suffixtree.o source/datastructures/qualityscores.o source/datastructures/groupmap.o source/datastructures/sequenceparser.o source/datastructures/reportfile.o source/datastructures/sequencecountparser.o source/datastructures/oligos.o source/datastructures/treemap.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundfloatvector.o source/datastructures/ordervector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/sharedrabundvector.o source/datastructures/database.o source/datastructures/designmap.o source/datastructures/sharedsabundvector.o source/datastructures/alignment.o source/datastructures/tree.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/decisiontree.o source/randomforest/abstractdecisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readblast.o source/read/readcluster.o source/read/readtree.o source/read/formatphylip.o source/read/readcolumn.o source/read/treereader.o source/read/readphylip.o source/svm/svm.o -lreadline -lboost_iostreams -lz
+g++ -Wl,-z,relro -Wl,-z,now -L "\"Enter_your_boost_library_path_here\"" -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/randomnumber.o source/gotohoverlap.o source/validparameter.o source/rarefact.o source/heatmap.o source/nast.o source/validcalculator.o source/mothurout.o source/completelinkage.o source/averagelinkage.o source/seqnoise.o source/vsearchfileparser.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/noalign.o source/collect.o source/trialSwap2.o source/sharedutilities.o source/consensus.o source/fileoutput.o source/cluster.o source/nastreport.o source/needlemanoverlap.o source/myseqdist.o source/refchimeratest.o source/subsample.o source/commandfactory.o source/rarecalc.o source/weightedlinkage.o source/wilcox.o source/progress.o source/linearalgebra.o source/singlelinkage.o source/trimoligos.o source/optionparser.o source/mothur.o source/engine.o source/slibshuff.o source/dlibshuff.o source/heatmapsim.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/overlap.o source/calculators/coverage.o source/calculators/structchi2.o source/calculators/shannonrange.o source/calculators/sharedace.o source/calculators/sharedthetan.o source/calculators/bergerparker.o source/calculators/hamming.o source/calculators/sharedsobs.o source/calculators/shen.o source/calculators/canberra.o source/calculators/parsimony.o source/calculators/gower.o source/calculators/smithwilson.o source/calculators/simpson.o source/calculators/mempearson.o source/calculators/logsd.o source/calculators/calculator.o source/calculators/goodscoverage.o source/calculators/memchord.o source/calculators/manhattan.o source/calculators/geom.o source/calculators/jackknife.o source/calculators/efron.o source/calculators/sharedrjsd.o source/calculators/bootstrap.o source/calculators/shannon.o source/calculators/invsimpson.o source/calculators/sharedsorclass.o source/calculators/sharedbraycurtis.o source/calculators/boneh.o source/calculators/npshannon.o source/calculators/structeuclidean.o source/calculators/sharedchao1.o source/calculators/qstat.o source/calculators/chao1.o source/calculators/simpsoneven.o source/calculators/whittaker.o source/calculators/sharedsobscollectsummary.o source/calculators/spearman.o source/calculators/structchord.o source/calculators/shannoneven.o source/calculators/sharedmorisitahorn.o source/calculators/bstick.o source/calculators/sharedjackknife.o source/calculators/solow.o source/calculators/sharedjsd.o source/calculators/sharedjest.o source/calculators/sharedsorabund.o source/calculators/sharedanderbergs.o source/calculators/prng.o source/calculators/odum.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedlennon.o source/calculators/memeuclidean.o source/calculators/memchi2.o source/calculators/sharedjabund.o source/calculators/unweighted.o source/calculators/uvest.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedjclass.o source/calculators/sharedkulczynskicody.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/weighted.o source/calculators/sharedkstest.o source/calculators/hellinger.o source/calculators/sharedochiai.o source/calculators/sharedkulczynski.o source/calculators/sharedthetayc.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimerarealigner.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/clearcut/getopt_long.o source/clearcut/cmdargs.o source/commands/listseqscommand.o source/commands/clusterdoturcommand.o source/commands/getlistcountcommand.o source/commands/setlogfilecommand.o source/commands/distancecommand.o source/commands/mergetaxsummarycommand.o source/commands/quitcommand.o source/commands/subsamplecommand.o source/commands/indicatorcommand.o source/commands/mgclustercommand.o source/commands/seqsummarycommand.o source/commands/getgroupscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/venncommand.o source/commands/renameseqscommand.o source/commands/setseedcommand.o source/commands/makegroupcommand.o source/commands/removerarecommand.o source/commands/classifyseqscommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/listotulabelscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/mimarksattributescommand.o source/commands/createdatabasecommand.o source/commands/splitgroupscommand.o source/commands/sffmultiplecommand.o source/commands/treegroupscommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/chimerabellerophoncommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/systemcommand.o source/commands/seqerrorcommand.o source/commands/aligncommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/libshuffcommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/getsharedotucommand.o source/commands/parsefastaqcommand.o source/commands/cooccurrencecommand.o source/commands/screenseqscommand.o source/commands/parsimonycommand.o source/commands/chimeraperseuscommand.o source/commands/sracommand.o source/commands/amovacommand.o source/commands/makelefsecommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getrabundcommand.o source/commands/catchallcommand.o source/commands/clusterfragmentscommand.o source/commands/mantelcommand.o source/commands/matrixoutputcommand.o source/commands/makecontigscommand.o source/commands/makefastqcommand.o source/commands/makelookupcommand.o source/commands/rarefactcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/chimeravsearchcommand.o source/commands/trimseqscommand.o source/commands/nmdscommand.o source/commands/collectsharedcommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/removeotulabelscommand.o source/commands/removeotuscommand.o source/commands/phylodiversitycommand.o source/commands/filtersharedcommand.o source/commands/shhhercommand.o source/commands/removegroupscommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/clearcutcommand.o source/commands/pcacommand.o source/commands/metastatscommand.o source/commands/chopseqscommand.o source/commands/sffinfocommand.o source/commands/makebiomcommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/corraxescommand.o source/commands/binsequencecommand.o source/commands/preclustercommand.o source/commands/setdircommand.o source/commands/chimeraccodecommand.o source/commands/classifytreecommand.o source/commands/deconvolutecommand.o source/commands/getseqscommand.o source/commands/deuniqueseqscommand.o source/commands/getmimarkspackagecommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/sharedcommand.o source/commands/mergefilecommand.o source/commands/getotuscommand.o source/commands/pcoacommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/getgroupcommand.o source/commands/helpcommand.o source/commands/pcrseqscommand.o source/commands/anosimcommand.o source/commands/deuniquetreecommand.o source/commands/classifyotucommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/removedistscommand.o source/commands/homovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/chimeracheckcommand.o source/commands/clustersplitcommand.o source/commands/pairwiseseqscommand.o source/commands/mergegroupscommand.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/nocommands.o source/commands/sparcccommand.o source/commands/heatmapcommand.o source/commands/phylotypecommand.o source/commands/rarefactsharedcommand.o source/commands/newcommandtemplate.o source/commands/shhhseqscommand.o source/commands/clustercommand.o source/commands/summarycommand.o source/commands/reversecommand.o source/commands/getcurrentcommand.o source/commands/collectcommand.o source/commands/getcommandinfocommand.o source/commands/kruskalwalliscommand.o source/commands/chimeraslayercommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/ordervector.o source/datastructures/sharedlistvector.o source/datastructures/fastamap.o source/datastructures/distancedb.o source/datastructures/alignment.o source/datastructures/sharedordervector.o source/datastructures/nameassignment.o source/datastructures/fastqread.o source/datastructures/kmer.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/counttable.o source/datastructures/kmeralign.o source/datastructures/sequenceparser.o source/datastructures/sparsematrix.o source/datastructures/alignmentdb.o source/datastructures/fullmatrix.o source/datastructures/blastalign.o source/datastructures/treenode.o source/datastructures/alignmentcell.o source/datastructures/suffixdb.o source/datastructures/sabundvector.o source/datastructures/rabundvector.o source/datastructures/suffixtree.o source/datastructures/qualityscores.o source/datastructures/groupmap.o source/datastructures/sparsedistancematrix.o source/datastructures/sequencecountparser.o source/datastructures/oligos.o source/datastructures/treemap.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/database.o source/datastructures/designmap.o source/datastructures/sharedsabundvector.o source/datastructures/tree.o source/datastructures/reportfile.o source/datastructures/listvector.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/abstractdecisiontree.o source/randomforest/decisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readblast.o source/read/readcluster.o source/read/treereader.o source/read/readtree.o source/read/formatphylip.o source/read/readcolumn.o source/read/readphylip.o source/svm/svm.o -lreadline -lboost_iostreams -lz
make[2]: Leaving directory '/build/mothur-1.38.1.1'
# cp mothur mothur-mpi # XXX: debug
make[1]: Leaving directory '/build/mothur-1.38.1.1'
@@ -1837,12 +1851,14 @@
dpkg-source --after-build mothur-1.38.1.1
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/6570/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/6570/tmp/hooks/B01_cleanup finished
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/25666 and its subdirectories
-I: Current time: Sat Dec 24 22:13:02 -12 2016
-I: pbuilder-time-stamp: 1482660782
+I: removing directory /srv/workspace/pbuilder/6570 and its subdirectories
+I: Current time: Mon Dec 26 01:22:04 +14 2016
+I: pbuilder-time-stamp: 1482664924
Compressing the 2nd log...
/var/lib/jenkins/userContent/reproducible/debian/logdiffs/testing/armhf/mothur_1.38.1.1-1.diff: 96.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/testing/armhf/mothur_1.38.1.1-1.diff.gz
b2/build.log: 94.9%
+ echo 'Compressing the 1st log...'
Compressing the 1st log...
+ gzip -9cvn b1/build.log
b1/build.log: 95.0%
+ chmod 644 /var/lib/jenkins/userContent/reproducible/debian/logs/testing/armhf/mothur_1.38.1.1-1.build1.log.gz
+ update_rbuildlog
+ chmod 644 /srv/reproducible-results/rbuild-debian-L5mxKNrm/tmp.hyzYQ5ExWU
+ mv /srv/reproducible-results/rbuild-debian-L5mxKNrm/tmp.hyzYQ5ExWU /var/lib/jenkins/userContent/reproducible/debian/rbuild/testing/armhf/mothur_1.38.1.1-1.rbuild.log
+ RBUILDLOG=/var/lib/jenkins/userContent/reproducible/debian/rbuild/testing/armhf/mothur_1.38.1.1-1.rbuild.log
+ '[' 0 -eq 1 ']'
+ '[' 0 -eq 0 ']'
+ filter_changes_files
+ sed -i -e '/^ [a-f0-9]\{32,64\} .*\.buildinfo$/d' b1/mothur_1.38.1.1-1_armhf.changes b2/mothur_1.38.1.1-1_armhf.changes
+ call_diffoscope_on_changes_files
++ mktemp --tmpdir=/srv/reproducible-results/rbuild-debian-L5mxKNrm
+ local TMPLOG=/srv/reproducible-results/rbuild-debian-L5mxKNrm/tmp.9hqeK3FbE9
+ local TIMEOUT=120m
+ DBDSUITE=testing
+ '[' testing = experimental ']'
+ set -x
++ mktemp --tmpdir=/srv/reproducible-results/rbuild-debian-L5mxKNrm -d dbd-tmp-XXXXXXX
+ local TEMP=/srv/reproducible-results/rbuild-debian-L5mxKNrm/dbd-tmp-GZoXGY5
++ schroot --directory /srv/reproducible-results/rbuild-debian-L5mxKNrm -c source:jenkins-reproducible-testing-diffoscope diffoscope -- --version
+ DIFFOSCOPE='diffoscope 64'
++ echo diffoscope 64
++ grep '^E: 15binfmt: update-binfmts: unable to open'
++ true
+ LOG_RESULT=
+ '[' '!' -z '' ']'
+ log_info 'diffoscope 64 will be used to compare the two builds:'
+ _log I: 'diffoscope 64 will be used to compare the two builds:'
+ local prefix=I:
+ shift 1
+ tee -a /var/lib/jenkins/userContent/reproducible/debian/rbuild/testing/armhf/mothur_1.38.1.1-1.rbuild.log
++ date -u
+ echo -e 'Sun Dec 25 11:25:40 UTC 2016 I: diffoscope 64 will be used to compare the two builds:'
Sun Dec 25 11:25:40 UTC 2016 I: diffoscope 64 will be used to compare the two builds:
+ set +e
+ set -x
+ timeout 120m nice schroot --directory /srv/reproducible-results/rbuild-debian-L5mxKNrm -c source:jenkins-reproducible-testing-diffoscope -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian-L5mxKNrm/dbd-tmp-GZoXGY5 ; diffoscope --html /srv/reproducible-results/rbuild-debian-L5mxKNrm/mothur_1.38.1.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian-L5mxKNrm/mothur_1.38.1.1-1.diffoscope.txt /srv/reproducible-results/rbuild-debian-L5mxKNrm/b1/mothur_1.38.1.1-1_armhf.changes /srv/reproducible-results/rbuild-debian-L5mxKNrm/b2/mothur_1.38.1.1-1_armhf.changes'
FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1720)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:404)
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