#59895 closed defect (duplicate)

atlas: xatlas_build segfaults

Reported by: nolaaa Owned by: Veence (Vincent)
Priority: Normal Milestone:
Component: ports Version: 2.6.2
Keywords: Cc:
Port: atlas

Description

I am trying to install an Astronomical package (source-extractor) which requires atlas to be pre-installed. I am running MacPorts 2.6.2 , Xcode 11.3, and gcc9. However, I keep getting an error that atlas fails to build. I also tried sudo port clean atlas but still get the same error. Here is the log of what I am doing:

sudo port install source-extractor
--->  Computing dependencies for source-extractor
The following dependencies will be installed: 
 atlas
 autoconf
 automake
 fftw-3
 fftw-3-single
 libtool
Continue? [Y/n]: 
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from https://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from http://aus.us.packages.macports.org/macports/packages/atlas
--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from http://kmq.jp.packages.macports.org/atlas
--->  Fetching distfiles for atlas
--->  Verifying checksums for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /usr/bin/clang
Selected F77 compiler: gfortran9
Warning: reinplace s|-no-cpp-precomp||g didn't change anything in /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt
--->  Building atlas
Error: Failed to build atlas: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port source-extractor failed

Also here is the full report of this error in my /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.logfile:

:debug:build build phase started at Fri Dec 27 13:51:19 PST 2019
:notice:build --->  Building atlas
:debug:build Executing org.macports.build (atlas)
:debug:build port disallows a parallel build
:debug:build Environment: 
:debug:build CC='/usr/bin/clang'
:debug:build CC_PRINT_OPTIONS='YES'
:debug:build CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/.CC_PRINT_OPTIONS'
:debug:build CPATH='/opt/local/include'
:debug:build CXX='/usr/bin/clang++'
:debug:build DEVELOPER_DIR='/Library/Developer/CommandLineTools'
:debug:build LIBRARY_PATH='/opt/local/lib'
:debug:build MACOSX_DEPLOYMENT_TARGET='10.15'
:debug:build SDKROOT='/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk'
:info:build Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build" && /usr/bin/make -w build 
:debug:build system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build" && /usr/bin/make -w build 
:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build'
:info:build /Library/Developer/CommandLineTools/usr/bin/make -f Make.top build
:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build'
:info:build cd bin/ ; /Library/Developer/CommandLineTools/usr/bin/make xatlas_build
:info:build make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/bin'
:info:build /usr/bin/clang -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei3 -DATL_CPUMHZ=2900 -DATL_AVXMAC -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2900 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -march=native -mfma  -c /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_tee.c
:info:build /usr/bin/clang -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei3 -DATL_CPUMHZ=2900 -DATL_AVXMAC -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2900 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -march=native -mfma  -o xatlas_tee atlas_tee.o
:info:build /usr/bin/clang -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei3 -DATL_CPUMHZ=2900 -DATL_AVXMAC -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2900 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -march=native -mfma  -c /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c
:info:build In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:38:
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_r1parse.h:879:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
:info:build    while (ln = GetJoinedLines(fpin))
:info:build           ~~~^~~~~~~~~~~~~~~~~~~~~~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_r1parse.h:879:14: note: place parentheses around the assignment to silence this warning
:info:build    while (ln = GetJoinedLines(fpin))
:info:build              ^
:info:build           (                        )
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_r1parse.h:879:14: note: use '==' to turn this assignment into an equality comparison
:info:build    while (ln = GetJoinedLines(fpin))
:info:build              ^
:info:build              ==
:info:build In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:39:
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_mvparse.h:914:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
:info:build    while (ln = GetJoinedLines(fpin))
:info:build           ~~~^~~~~~~~~~~~~~~~~~~~~~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_mvparse.h:914:14: note: place parentheses around the assignment to silence this warning
:info:build    while (ln = GetJoinedLines(fpin))
:info:build              ^
:info:build           (                        )
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_mvparse.h:914:14: note: use '==' to turn this assignment into an equality comparison
:info:build    while (ln = GetJoinedLines(fpin))
:info:build              ^
:info:build              ==
:info:build In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:40:
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_mmparse.h:1011:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
:info:build    while (ln = GetJoinedLines(fpin))
:info:build           ~~~^~~~~~~~~~~~~~~~~~~~~~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_mmparse.h:1011:14: note: place parentheses around the assignment to silence this warning
:info:build    while (ln = GetJoinedLines(fpin))
:info:build              ^
:info:build           (                        )
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/atlas_mmparse.h:1011:14: note: use '==' to turn this assignment into an equality comparison
:info:build    while (ln = GetJoinedLines(fpin))
:info:build              ^
:info:build              ==
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:148:22: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
:info:build    for (i=0; str0[i] = str[i]; i++);
:info:build              ~~~~~~~~^~~~~~~~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:148:22: note: place parentheses around the assignment to silence this warning
:info:build    for (i=0; str0[i] = str[i]; i++);
:info:build                      ^
:info:build              (               )
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:148:22: note: use '==' to turn this assignment into an equality comparison
:info:build    for (i=0; str0[i] = str[i]; i++);
:info:build                      ^
:info:build                      ==
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:267:25: warning: length modifier 'L' results in undefined behavior or no effect with 'd' conversion specifier [-Wformat]
:info:build          sscanf(ln+i, "%Ld", &iret);
:info:build                        ~^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:267:25: note: did you mean to use 'll'?
:info:build          sscanf(ln+i, "%Ld", &iret);
:info:build                         ^
:info:build                         ll
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:281:30: warning: format specifies type 'unsigned long *' but the argument has type 'long long *' [-Wformat]
:info:build          sscanf(ln+i, "%lx", &iret);
:info:build                        ~~~   ^~~~~
:info:build                        %llx
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:486:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build       fprintf(fp0, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:486:20: note: treat the string as an argument to avoid this
:info:build       fprintf(fp0, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:488:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build       fprintf(fp1, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:488:20: note: treat the string as an argument to avoid this
:info:build       fprintf(fp1, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:684:16: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations]
:info:build    ATL_Cassert(tmpnam(tnam), "GETTING TEMPFILE", NULL);
:info:build                ^
:info:build /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdio.h:186:1: note: 'tmpnam' has been explicitly marked deprecated here
:info:build __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead.")
:info:build ^
:info:build /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/cdefs.h:191:48: note: expanded from macro '__deprecated_msg'
:info:build         #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
:info:build                                                       ^
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:779:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build             fprintf(stdout, ln);
:info:build                             ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:779:29: note: treat the string as an argument to avoid this
:info:build             fprintf(stdout, ln);
:info:build                             ^
:info:build                             "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:783:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:783:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:839:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:839:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:857:32: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build                fprintf(stdout, ln);
:info:build                                ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:857:32: note: treat the string as an argument to avoid this
:info:build                fprintf(stdout, ln);
:info:build                                ^
:info:build                                "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:884:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build       fprintf(stdout, ln);
:info:build                       ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:884:23: note: treat the string as an argument to avoid this
:info:build       fprintf(stdout, ln);
:info:build                       ^
:info:build                       "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:899:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:899:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:925:29: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build             fprintf(stdout, ln);
:info:build                             ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:925:29: note: treat the string as an argument to avoid this
:info:build             fprintf(stdout, ln);
:info:build                             ^
:info:build                             "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:958:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:958:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:973:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:973:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:979:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:979:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:983:23: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build       fprintf(stdout, ln);
:info:build                       ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:983:23: note: treat the string as an argument to avoid this
:info:build       fprintf(stdout, ln);
:info:build                       ^
:info:build                       "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:996:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:996:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1029:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1029:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1064:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1064:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1102:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build    fprintf(stdout, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1102:20: note: treat the string as an argument to avoid this
:info:build    fprintf(stdout, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1113:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build    fprintf(stdout, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1113:20: note: treat the string as an argument to avoid this
:info:build    fprintf(stdout, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1124:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build    fprintf(stdout, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1124:20: note: treat the string as an argument to avoid this
:info:build    fprintf(stdout, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1132:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build    fprintf(stdout, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1132:20: note: treat the string as an argument to avoid this
:info:build    fprintf(stdout, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1147:26: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build          fprintf(stdout, ln);
:info:build                          ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1147:26: note: treat the string as an argument to avoid this
:info:build          fprintf(stdout, ln);
:info:build                          ^
:info:build                          "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1165:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build    fprintf(stdout, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1165:20: note: treat the string as an argument to avoid this
:info:build    fprintf(stdout, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1175:20: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
:info:build    fprintf(stdout, ln);
:info:build                    ^~
:info:build /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//bin/atlas_install.c:1175:20: note: treat the string as an argument to avoid this
:info:build    fprintf(stdout, ln);
:info:build                    ^
:info:build                    "%s", 
:info:build 30 warnings generated.
:info:build /usr/bin/clang -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Corei3 -DATL_CPUMHZ=2900 -DATL_AVXMAC -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DATL_DYLIBS -DPentiumCPS=2900 -DATL_FULL_LAPACK -DATL_NCPU=4 -O3 -fomit-frame-pointer -fPIC -march=native -mfma  -o xatlas_build atlas_install.o
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/bin'
:info:build cd bin/ ; ./xatlas_build -1 0 -a 1 -l 1
:info:build /bin/sh: line 1: 66976 Segmentation fault: 11  ./xatlas_build -1 0 -a 1 -l 1
:info:build make[1]: *** [build] Error 139
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build'
:info:build make: *** [build] Error 2
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build" && /usr/bin/make -w build 
:info:build Exit code: 2
:error:build Failed to build atlas: command execution failed
:debug:build Error code: CHILDSTATUS 66962 2
:debug:build Backtrace: command execution failed
:debug:build     while executing
:debug:build "system {*}$notty {*}$nice $fullcmdstring"
:debug:build     invoked from within
:debug:build "command_exec build"
:debug:build     (procedure "portbuild::build_main" line 8)
:debug:build     invoked from within
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log for details.

Change History (2)

comment:1 Changed 10 months ago by ryandesign (Ryan Schmidt)

Owner: set to Veence
Port: atlas added
Status: newassigned
Summary: atlas fails to install with "command execution failed"atlas: xatlas_build segfaults

Looks like a duplicate of #59269.

comment:2 Changed 10 months ago by ryandesign (Ryan Schmidt)

Resolution: duplicate
Status: assignedclosed
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