<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yiv0059375724yui_3_16_0_1_1452700096952_12440" class=""><span id="yiv0059375724yui_3_16_0_1_1452700096952_12473" class="" style="font-family: Helvetica; font-size: 12px;">I am installing Biopython on MacOSX. “gcc” fails to find “stdio.h” file. I am running MacOSX version 10.11.2 (ElCapitan).</span></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12475" style="font-family: Helvetica; font-size: 12px;" dir="ltr">I tried "pip install biopython” and then tried installing from source. gcc fails in both cases. I get the following error message:</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12477" style="font-family: Helvetica; font-size: 12px;"><br class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12479"></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12481" style="font-family: Helvetica; font-size: 12px;"><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12483" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -Qunused-arguments -Qunused-arguments -I/Applications/Canopy.app/appdata/canopy-1.5.2.2785.macosx-x86_64/Canopy.app/Contents/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.6-x86_64-2.7/Bio/cpairwise2module.o</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12485" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.6.sdk'</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12487" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">In file included from Bio/cpairwise2module.c:12:</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12489" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">/Applications/Canopy.app/appdata/canopy-1.5.2.2785.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h:33:10: <span class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12491" style="color: rgb(195, 55, 32);">fatal error: </span></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12493" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;"> 'stdio.h' file not found</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12495" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">#include <stdio.h></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12497" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(52, 189, 38);"> ^</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12499" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">1 error generated.</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12501" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">error: command 'gcc' failed with exit status 1</div></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12503" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;"><br class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12505"></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12507" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">Similar failure occurs with pip install.</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12509" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;"><br class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12511"></div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12513" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">Any help will be appreciated. I have python 2.7 with Canopy installed on the system.</div><div class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12515" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;"><br class="" id="yiv0059375724yui_3_16_0_1_1452700096952_12517"></div><div class="" dir="ltr" id="yiv0059375724yui_3_16_0_1_1452700096952_12519" style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco;">Ravi Tavakley</div></div></body></html>