Fix compilation things from Jakub

[psathyrella]

 These are fixes for reading the environment variables.

--- a/packages/ham/src/SConscript
+++ b/packages/ham/src/SConscript
@@ -2,7 +2,7 @@ import os
 import sys
 import glob

-env = Environment()
+env = Environment(ENV=os.environ)

--- a/packages/ham/yaml-cpp/SConscript
+++ b/packages/ham/yaml-cpp/SConscript
@@ -2,7 +2,7 @@ import os
 import glob
 import sys

-env = Environment()
+env = Environment(ENV=os.environ)

More things

Got errors which I guess were related to compiler differences or quirkiness of this system, but I don't really know. Sorry I lost the error messages.

This one said something about missing 'keypad' and found this fix.

--- a/packages/samtools/Makefile
+++ b/packages/samtools/Makefile
@@ -122,7 +122,7 @@ libbam.a:$(LOBJS)
        $(AR) -csru $@ $(LOBJS)

 samtools: $(AOBJS) libbam.a $(HTSLIB)
-       $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+       $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz -ltinfo


I was missing static libraries this time:

--- a/packages/smctc/examples/rare-events/Makefile
+++ b/packages/smctc/examples/rare-events/Makefile
@@ -5,7 +5,7 @@ O = main.o simfunctions.o
 H = simfunctions.hh

 CCFLAGS := $(CCFLAGS) -I../../include -L../../lib
-LFLAGS := -g -I../../include -L../../lib -static $(LFLAGS)
+LFLAGS := -g -I../../include -L../../lib $(LFLAGS)


Had to comment out this in bin/build.sh, because it thought i was in docker when i wasn't. Don't know how its failing.

--- a/bin/build.sh
+++ b/bin/build.sh
@@ -1,11 +1,11 @@
 echo -e "\n--> running $0"
 set -eu

-if grep -v '/$' /proc/1/cgroup>/dev/null; then
-    basedir=/partis  # if we're in docker
-else
+#if grep -v '/$' /proc/1/cgroup>/dev/null; then
+#    basedir=/partis  # if we're in docker
+#else
     basedir=$PWD
-fi
+#fi

[psathyrella]

@jotwin thanks for the suggestions. I've put in the first two scons env things, and switched to a different way of checking if we're inside docker. I can't seem to google enough about the -ltinfo and -static options to figure out if I should add them to the master branch... so unless you think I should, I think I'll leave them out and figure they're peculiar to your system?

[jotwin]

Yeah you should leave them out. The tinfo was from using an old gcc, and the -static was from missing gsl static libraries.

[psathyrella]

Ah, cool, thanks.