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<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
Dear support,</div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
<br>
</div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
I�ve been wrestling with building exm v0.8.0 on our RHEL 6.0 Linux system. I�m using gcc v4.9.1.</div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
<br>
</div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
When building the Turbine package it fails with the following:</div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
<br>
</div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
<snip></div>
<div>
<div><font color="#183669" face="Candara,sans-serif">Preparing config files: please wait...</font></div>
<div><font color="#183669" face="Candara,sans-serif">configure: creating ./config.status</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/turbine/turbine-version.h</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/turbine/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/util/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/util/debug-tokens.tcl</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/adlb/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/blob/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/c-utils/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/mpe/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/julia/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/python/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/r/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/static-pkg/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/turbine/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/executables/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating lib/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/main-wrap/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/cobalt/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/cray/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/ec2/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/pbs/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/slurm/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/turbine-config.sh</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/turbine-build-config.sh</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating tests/module.mk</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating tests/runbin.zsh</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating Makefile</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating config.h</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: config.h is unchanged</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC_DEPS<span class="Apple-tab-span" style="white-space:pre">
</span>src/executables/turbine_sh.manifest.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/static-pkg/static-pkg.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC_DEPS<span class="Apple-tab-span" style="white-space:pre">
</span>tests/staticapp-bundled-1.manifest.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC_DEPS<span class="Apple-tab-span" style="white-space:pre">
</span>tests/staticapp-1.manifest.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> TCL<span class="Apple-tab-span" style="white-space:pre">
</span>src/util/debug.h</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC<span class="Apple-tab-span" style="white-space:pre">
</span>src/executables/turbine_sh.c</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/turbine/tcl-turbine.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/adlb/tcl-adlb.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/julia/tcl-julia.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/util/debug.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/executors/noop_executor.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/async_exec.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/worker.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/cache.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/turbine.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span class="Apple-tab-span" style="white-space:pre">
</span>src/executables/turbine_sh.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/static-pkg/static-pkg.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/turbine.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/cache.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/worker.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/executors/noop_executor.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/turbine/async_exec.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/util/debug.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/julia/tcl-julia.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span class="Apple-tab-span" style="white-space:pre">
</span>src/tcl/adlb/tcl-adlb.o</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/executors/noop_executor.c: In function �noop_execute�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/executors/noop_executor.c:174:8: warning: variable �found_slot� set but not used [-Wunused-but-set-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> bool found_slot = false;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/worker.c: In function �task_error�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/worker.c:102:7: warning: unused variable �rc� [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc = asprintf(&msg, "\n%s%s", prefix, command);</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c: In function �launch_error�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c:482:7: warning: unused variable �rc� [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc = asprintf(&msg, "Turbine %s worker task error in: %s",</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c: In function �callback_error�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c:501:7: warning: unused variable �rc� [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc = asprintf(&msg, "Turbine %s worker task error in callback: %s",</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif"> AR<span class="Apple-tab-span" style="white-space:pre">
</span>lib/libtclturbinestatic.a</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �adlb_setup_comm�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:384:7: warning: variable �rc� set but not used [-Wunused-but-set-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �tcl_dict_to_packed_container�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2132:1: warning: label �exit_err� defined but not used [-Wunused-label]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> exit_err:</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �tcl_list_to_packed_multiset�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2192:1: warning: label �exit_err� defined but not used [-Wunused-label]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> exit_err:</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �packed_struct_to_tcl_dict�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2247:17: warning: unused variable �name� [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> const char *name = field_names[i];</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �get_compound_type�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5100:1: warning: label �exit_err� defined but not used [-Wunused-label]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> exit_err:</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �ADLB_Subscript_Impl�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5645:11: warning: unused variable �sub� [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> char *sub = Tcl_GetStringFromObj(objv[i + 2], &sub_len);</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �adlb_datum2tclobj�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2707:22: warning: �tmp.value� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_datum_storage tmp;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2739:17: warning: �tmp.length� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> *result = Tcl_NewStringObj(tmp.STRING.value,</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �ADLB_Enumerate_Cmd�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:3017:8: warning: �include_vals� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> bool include_vals;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:3016:8: warning: �include_keys� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> bool include_keys;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �ADLB_Refcount_Incr_Cmd�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:4791:22: warning: �mode� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_refcount_type mode;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �ADLB_Parse_Subscript�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5498:15: warning: �tmp_sub.length� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> sub->length += to_append.length;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5404:22: note: �tmp_sub.length� was declared here</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_subscript tmp_sub;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function �ADLB_Create_Nested_Impl.isra.52�:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:4340:8: warning: �retrieved.write_refs� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> if (retrieved.write_refs <= 0)</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">In file included from src/tcl/adlb/tcl-adlb.c:71:0:</font></div>
<div><font color="#183669" face="Candara,sans-serif">./src/tcl/util.h:164:5: warning: �retrieved.id� may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> turbine_tcl_condition_failed(interp, objv[0], format, ## args); \</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:4333:14: note: �retrieved.id� was declared here</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_ref retrieved;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">exm-setup.zsh: turbine: build FAILED</font></div>
</div>
<div><font color="#183669" face="Candara,sans-serif"></snip></font></div>
<div><font color="#183669" face="Candara,sans-serif"><br>
</font></div>
<div><font color="#183669" face="Candara,sans-serif">I</font><font color="#183669" face="Candara,sans-serif"> see various warnings but no errors in the above</font><font color="#183669" face="Candara,sans-serif">�yet the setup fails. I would be grateful if
you could provide some assistance in diagnosing what is happening.</font></div>
<div><font color="#183669" face="Candara,sans-serif"><br>
</font></div>
<div><font color="#183669" face="Candara,sans-serif">Much appreciated,</font></div>
<div><font color="#183669" face="Candara,sans-serif"><br>
</font></div>
<div><font color="#183669" face="Candara,sans-serif">Tim.</font></div>
<div style="color: rgb(24, 54, 105); font-family: Candara, sans-serif; font-size: 14px;">
<p style="font-size: 12px; margin: 0px; font-family: Verdana;">---</p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;"><b>Timothy Stitt PhD</b> / Head of Scientific Computing</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">The Genome Analysis Centre (TGAC), Room 204b</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(4, 46, 238);"><span style="text-decoration: underline; font-size: 10px;"><a href="http://www.tgac.ac.uk/">http://www.tgac.ac.uk/</a></span></p>
<p style="margin: 0px; font-family: Cambria; min-height: 19px;"><span style="font-size: 10px;"><br>
</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">p: +44 1603 450378</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(13, 102, 213);"><span style="color: rgb(0, 0, 0); font-size: 10px;">e: <a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a></span></p>
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