aboutsummaryrefslogtreecommitdiff
path: root/reproduce/software/shell/configure.sh
blob: f4284166751a3dd21236f4c7560038007cf3a899 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
#!/bin/sh
#
# Necessary preparations/configurations for the reproducible project.
#
# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This script is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this script.  If not, see <http://www.gnu.org/licenses/>.





# Script settings
# ---------------
# Stop the script if there are any errors.
set -e





# Internal directories
# --------------------
#
# These are defined to help make this script more readable.
topdir=$(pwd)
optionaldir="/optional/path"
adir=reproduce/analysis/config
cdir=reproduce/software/config

pconf=$cdir/LOCAL.conf
ptconf=$cdir/LOCAL_tmp.conf
poconf=$cdir/LOCAL_old.conf
depverfile=$cdir/versions.conf
depshafile=$cdir/checksums.conf
# --------- Delete for no Gnuastro ---------
glconf=$adir/gnuastro/gnuastro-local.conf
# ------------------------------------------





# Notice for top of generated files
# ---------------------------------
#
# In case someone opens the files output from the configuration scripts in
# a text editor and wants to edit them, it is important to let them know
# that their changes are not going to be permenant.
create_file_with_notice ()
{
    if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
    then
        echo "#"                                                      >> "$1"
        echo "# This file was created during configuration"           >> "$1"
        echo "# ('./project configure'). Therefore, it is not under"  >> "$1"
        echo "# version control and any manual changes to it will be" >> "$1"
        echo "# over-written if the project re-configured."           >> "$1"
        echo "#"                                                      >> "$1"
    else
        echo; echo "Can't write to $1"; echo;
        exit 1
    fi
}





# Get absolute address
# --------------------
#
# Since the build directory will go into a symbolic link, we want it to be
# an absolute address. With this function we can make sure of that.
absolute_dir ()
{
    if stat "$1" 1> /dev/null; then
        echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
    else
        exit 1;
    fi
}





# Check file permission handling (POSIX-compatibility)
# ----------------------------------------------------
#
# Check if a `given' directory handles permissions as expected.
#
# This is to prevent a known bug in the NTFS filesystem that prevents
# proper installation of Perl, and probably some other packages. This
# function receives the directory as an argument and then, creates a dummy
# file, and examines whether the given directory handles the file
# permissions as expected.
#
# Returns `0' if everything is fine, and `255' otherwise. Choosing `0' is
# to mimic the `$ echo $?' behavior, while choosing `255' is to prevent
# misunderstanding 0 and 1 as true and false.
#
# ===== CAUTION! ===== #
#
# Since there is a `set -e' before running this function, the whole script
# stops and exits IF the `check_permission' (or any other function) returns
# anything OTHER than `0'! So, only use this function as a test. Here's a
# minimal example:
#
#     if $(check_permission $some_directory) ; then
#       echo "yay"; else "nay";
#     fi ;
check_permission ()
{
    # Make a `junk' file, activate its executable flag and record its
    # permissions generally.
    local junkfile=$1/check_permission_tmp_file
    rm -f $junkfile
    echo "Don't let my short life go to waste" > $junkfile
    chmod +x $junkfile
    local perm_before=$(ls -l $junkfile | awk '{print $1}')

    # Now, remove the executable flag and record the permissions.
    chmod -x $junkfile
    local perm_after=$(ls -l $junkfile | awk '{print $1}')

    # Clean up before leaving the function
    rm -f $junkfile

    # If the permissions are equal, the filesystem doesn't allow
    # permissions.
    if [ $perm_before = $perm_after ]; then
        # Setting permission FAILED
        return 1
    else
        # Setting permission SUCCESSFUL
	return 0
    fi
}





# Check if there is enough free space available in the build directory
# --------------------------------------------------------------------
#
# Use this function to check if there is enough free space in a
# directory. It is meant to be passed to the 'if' statement in the
# shell. So if there is enough space, it returns 0 (which translates to
# TRUE), otherwise, the funcion returns 1 (which translates to FALSE).
#
# Expects to be called with two arguments, the first is the threshold and
# the second is the desired directory. The 'df' function checks the given
# path to see where it is mounted on, and how much free space there is on
# that partition (in units of 1024 bytes).
#
# synopsis:
# $ free_space_warning <acceptable_threshold> <path-to-check>
#
# example:
# To check if there is 5MB of space available in /path/to/check
# call the command with arguments as shown below:
# $ free_space_warning 5000 /path/to/check/free/space
free_space_warning()
{
    fs_threshold=$1
    fs_destpath=$2
    return $(df $fs_destpath \
                | awk 'FNR==2 {if($4>'$fs_threshold') print 1; \
                               else                   print 0; }')
}





# Check for C/C++ compilers
# -------------------------
#
# To build the software, we'll need some basic tools (the compilers in
# particular) to be present.
hascc=0;
if type cc > /dev/null 2>/dev/null; then
    if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi
else
    if type gcc > /dev/null 2>/dev/null; then
        if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
    else
        if type clang > /dev/null 2>/dev/null; then
            if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi
        fi
    fi
fi
if [ $hascc = 0 ]; then
    cat <<EOF
______________________________________________________
!!!!!!!       C/C++ Compiler NOT FOUND         !!!!!!!

To build the project's software, the host system needs to have basic C and
C++ compilers. The executables that were checked are 'cc', 'gcc' and
'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
compiler. If you have a relevant compiler that is not checked, please get
in touch with us (with the form below) so we add it:

  https://savannah.nongnu.org/support/?func=additem&group=reproduce
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
    exit 1
fi





# Special directory for compiler testing
# --------------------------------------
#
# This directory will be deleted when the compiler testing is finished.
compilertestdir=.compiler_test_dir_please_delete
if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi





# Check C compiler
# ----------------
gcc_works=0
testprog=$compilertestdir/test
testsource=$compilertestdir/test.c
echo; echo; echo "Checking host C compiler...";
cat > $testsource <<EOF
#include <stdio.h>
#include <stdlib.h>
int main(void){printf("...C compiler works.\n");
               return EXIT_SUCCESS;}
EOF
if $CC $testsource -o$testprog && $testprog; then
    rm $testsource $testprog
else
    rm $testsource
    cat <<EOF

______________________________________________________
!!!!!!!        C compiler doesn't work         !!!!!!!

Host C compiler ('gcc') can't build a simple program.

A working C compiler is necessary for building the project's software.
Please use the error message above to find a good solution and re-run the
project configuration.

If you can't find a solution, please send the error message above to the
link below and we'll try to help

https://savannah.nongnu.org/support/?func=additem&group=reproduce

TIP: Once you find the solution, you can use the '-e' option to use
existing configuration:

   $ ./project configure -e

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
    exit 1
fi





# See if the linker accepts -Wl,-rpath-link
# -----------------------------------------
#
# `-rpath-link' is used to write the information of the linked shared
# library into the shared object (library or program). But some versions of
# LLVM's linker don't accept it an can cause problems.
cat > $testsource <<EOF
#include <stdio.h>
#include <stdlib.h>
int main(void) {return EXIT_SUCCESS;}
EOF
if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
    export rpath_command="-Wl,-rpath-link=$instdir/lib"
else
    export rpath_command=""
fi
rm -f $testprog $testsource





# See if we need the dynamic-linker (-ldl)
# ----------------------------------------
#
# Some programs (like Wget) need dynamic loading (using `libdl'). On
# GNU/Linux systems, we'll need the `-ldl' flag to link such programs.  But
# Mac OS doesn't need any explicit linking. So we'll check here to see if
# it is present (thus necessary) or not.
cat > $testsource <<EOF
#include <stdio.h>
#include <dlfcn.h>
int
main(void) {
    void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
    return 0;
}
EOF
if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
    needs_ldl=no;
else
    needs_ldl=yes;
fi
rm -f $testprog $testsource





# See if the C compiler can build static libraries
# ------------------------------------------------
#
# We are manually only working with shared libraries: because some
# high-level programs like Wget and cURL need dynamic linking and if we
# build the libraries statically, our own builds will be ignored and these
# programs will go and find their necessary libraries on the host system.
#
# Another good advantage of shared libraries is that we can actually use
# the shared library tool of the system (`ldd' with GNU C Library) and see
# exactly where each linked library comes from. But in static building,
# unless you follow the build closely, its not easy to see if the source of
# the library came from the system or our build.
static_build=no





# See if we are on a Linux-based system
# --------------------------------------
#
# Some features are tailored to GNU/Linux systems, while the BSD-based
# behavior is different. Initially we only tested macOS (hence the name of
# the variable), but as FreeBSD is also being inlucded in our tests. As
# more systems get used, we need to tailor these kinds of things better.
kernelname=$(uname -s)
if [ x$kernelname = xLinux ]; then
    on_mac_os=no
else
    host_cc=1
    on_mac_os=yes
fi





# Print warning if the host CC is to be used.
if [ x$host_cc = x1 ]; then
    cat <<EOF

______________________________________________________
!!!!!!!!!!!!!!!        Warning        !!!!!!!!!!!!!!!!

The GNU Compiler Collection (GCC, including compilers for C, C++, Fortran
and etc) is currently not built on macOS systems for this project. To build
the project's necessary software on this system, we need to use your
system's C compiler.

Project's configuration will continue in 5 seconds.
______________________________________________________

EOF
    sleep 5
fi




# Necessary C library element positions
# -------------------------------------
#
# On some systems (in particular Debian-based OSs), the static C library
# and necessary headers in a non-standard place, and we can't build GCC. So
# we need to find them first. The `sys/cdefs.h' header is also in a
# similarly different location.
sys_cpath=""
sys_library_path=""
if [ x"$$on_mac_os" != xyes ]; then

    # Get the GCC target name of the compiler, when its given, special
    # C libraries and headers are in a sub-directory of the host.
    gcctarget=$(gcc -v 2>&1 \
                    | tr ' ' '\n' \
                    | awk '/\-\-target/' \
                    | sed -e's/\-\-target=//')
    if [ x"$gcctarget" != x ]; then
        if [ -f /usr/lib/$gcctarget/libc.a ]; then
            export sys_library_path=/usr/lib/$gcctarget
            export sys_cpath=/usr/include/$gcctarget
        fi
    fi

    # For a check:
    #echo "sys_library_path: $sys_library_path"
    #echo "sys_cpath: $sys_cpath"
fi





# See if a link-able static C library exists
# ------------------------------------------
#
# A static C library and the `sys/cdefs.h' header are necessary for
# building GCC.
if [ x"$host_cc" = x0 ]; then
    echo; echo; echo "Checking if static C library is available...";
    cat > $testsource <<EOF
#include <stdio.h>
#include <stdlib.h>
#include <sys/cdefs.h>
int main(void){printf("...yes\n");
               return EXIT_SUCCESS;}
EOF
    cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
    if $cc_call && $testprog; then
        gccwarning=0
        rm $testsource $testprog
    else
        echo; echo "Compilation command:"; echo "$cc_call"
        rm $testsource
        gccwarning=1
        host_cc=1
        cat <<EOF

_______________________________________________________
!!!!!!!!!!!!            Warning            !!!!!!!!!!!!

The 'sys/cdefs.h' header cannot be included, or a usable static C library
('libc.a', in any directory) cannot be used with the current settings of
this system. SEE THE ERROR MESSAGE ABOVE.

Because of this, we can't build GCC. You either 1) don't have them, or 2)
the default system environment aren't enough to find them.

1) If you don't have them, your operating system provides them as separate
packages that you must manually install. Please look into your operating
system documentation or contact someone familiar with it. For example on
some Redhat-based GNU/Linux distributions, the static C library package can
be installed with this command:

    $ sudo yum install glibc-static

2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for
example in '/PATH/TO/STATIC/LIBC/libc.a' and
'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then
re-configure the project to fix this problem.

    $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
    $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"

_______________________________________________________

EOF
    fi
fi

# Print a warning if GCC is not meant to be built.
if [ x"$gccwarning" = x1 ]; then
        cat <<EOF

PLEASE SEE THE WARNINGS ABOVE.

Since GCC is pretty low-level, this configuration script will continue in 5
seconds and use your system's C compiler (it won't build a custom GCC). But
please consider installing the necessary package(s) to complete your C
compiler, then re-run './project configure'.

Project's configuration will continue in 5 seconds.

EOF
        sleep 5
fi





# Fortran compiler
# ----------------
#
# If GCC is ultimately build within the project, the user won't need to
# have a fortran compiler, we'll build it internally for high-level
# programs. However, when the host C compiler is to be used, the user needs
# to have a Fortran compiler available.
if [ $host_cc = 1 ]; then

    # See if a Fortran compiler exists.
    hasfc=0;
    if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
    if [ $hasfc = 0 ]; then
        cat <<EOF
______________________________________________________
!!!!!!!      Fortran Compiler NOT FOUND        !!!!!!!

The project won't be building its own GCC (which includes a Fortran
compiler) on this system. If you need software that need a Fortran
compiler, it will crash with an error. Fortran is necessary for many
lower-level scientific programs, hence this warning. Currently we search
for 'gfortran'. If you have a Fortran compiler that is not checked, please
get in touch with us (with the form below) so we add it:

  https://savannah.nongnu.org/support/?func=additem&group=reproduce

Project's configuration will continue in 5 seconds.
______________________________________________________

EOF
        sleep 5
    else

        # See if the Fortran compiler works
        testsource=$compilertestdir/test.f
        echo; echo; echo "Checking host Fortran compiler...";
        echo "      PRINT *, \"... Fortran Compiler works.\""  > $testsource
        echo "      END"                                      >> $testsource
        if gfortran $testsource -o$testprog && $testprog; then
            rm $testsource $testprog
        else
            rm $testsource
            cat <<EOF

______________________________________________________
!!!!!!!     Fortran compiler doesn't work      !!!!!!!

Host Fortran compiler ('gfortran') can't build a simple program.

A working Fortran compiler is necessary for building some of the project's
software.  Please use the error message above to find a good solution and
re-run the project configuration.

If you can't find a solution, please send the error message above to the
link below and we'll try to help

https://savannah.nongnu.org/support/?func=additem&group=reproduce

TIP: Once you find the solution, you can use the '-e' option to use
existing configuration:

   $ ./project configure -e

Project's configuration will continue in 5 seconds.
______________________________________________________

EOF
            sleep 5
        fi
    fi
fi





# Delete the compiler testing directory
# -------------------------------------
#
# This directory was made above to make sure the necessary compilers can be
# run.
rm -rf $compilertestdir





# Inform the user
# ---------------
#
# Print some basic information so the user gets a feeling of what is going
# on and is prepared on what will happen next.
cat <<EOF

-----------------------------
Project's local configuration
-----------------------------

Below, some basic local settings will be requested to start building
Maneage on this system (if they haven't been specified on the
command-line). This includes the top-level directories that Maneage will
use on your system. Most are only optional and you can simply press ENTER,
without giving any value (in this case, Maneage will download the necessary
components from pre-defined webpages). It is STRONGLY recommended to read
the description above each question before answering it.

EOF





# What to do with possibly existing configuration file
# ----------------------------------------------------
#
# `LOCAL.conf' is the top-most local configuration for the project. If it
# already exists when this script is run, we'll make a copy of it as backup
# (for example the user might have ran `./project configure' by mistake).
printnotice=yes
rewritepconfig=yes
rewritegconfig=yes
if [ -f $pconf ] || [ -f $glconf ]; then
    if [ $existing_conf = 1 ]; then
        printnotice=no
        if [ -f $pconf  ]; then rewritepconfig=no; fi
        if [ -f $glconf ]; then rewritegconfig=no; fi
    fi
fi




# Make sure the group permissions satisfy the previous configuration (if it
# exists and we don't want to re-write it).
if [ $rewritepconfig = no ]; then
    oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf)
    if [ "x$oldgroupname" = "x$reproducible_paper_group_name" ]; then
        just_a_place_holder_to_avoid_not_equal_test=1;
    else
        echo "-----------------------------"
        echo "!!!!!!!!    ERROR    !!!!!!!!"
        echo "-----------------------------"
        if [ "x$oldgroupname" = x ]; then
            status="NOT configured for groups"
            confcommand="./project configure"
        else
            status="configured for '$oldgroupname' group"
            confcommand="./project configure --group=$oldgroupname"
        fi
        echo "Project was previously $status!"
        echo "Either enable re-write of this configuration file,"
        echo "or re-run this configuration like this:"
        echo
        echo "   $confcommand"; echo
        exit 1
    fi
fi





# Identify the downloader tool
# ----------------------------
#
# After this script finishes, we will have both Wget and cURL for
# downloading any necessary dataset during the processing. However, to
# complete the configuration, we may also need to download the source code
# of some necessary software packages (including the downloaders). So we
# need to check the host's available tool for downloading at this step.
if [ $rewritepconfig = yes ]; then
    if type wget > /dev/null 2>/dev/null; then
        name=$(which wget)

        # By default Wget keeps the remote file's timestamp, so we'll have
        # to disable it manually.
        downloader="$name --no-use-server-timestamps -O";
    elif type curl > /dev/null 2>/dev/null; then
        name=$(which curl)

        # - cURL doesn't keep the remote file's timestamp by default.
        # - With the `-L' option, we tell cURL to follow redirects.
        downloader="$name -L -o"
    else
        cat <<EOF

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Couldn't find GNU Wget, or cURL on this system. These programs are used for
downloading necessary programs and data if they aren't already present (in
directories that you can specify with this configure script). Therefore if
the necessary files are not present, the project will crash.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
        downloader="no-downloader-found"
    fi;
fi





# Build directory
# ---------------
currentdir=$(pwd)
if [ $rewritepconfig = yes ]; then
    cat <<EOF

===============
Build directory
===============

The project's "source" (this directory) and "build" directories are treated
separately. This greatly helps in managing the many intermediate files that
are created during the build. The intermediate build files don't need to be
archived or backed up: you can always re-build them with the contents of
the source directory. The build directory also needs a relatively large
amount of free space (atleast serveral Giga-bytes), while the source
directory (all plain text) will usually be a mega-byte or less.

'.build' (a symbolic link to the build directory) will also be created
during this configuration. It can help encourage you to set the actual
build directory in a very different address from this one (one that can be
deleted and has large volume), while having easy access to it from here.

--- CAUTION ---
Do not choose any directory under the top source directory (this
directory). The build directory cannot be a subdirectory of the source.
---------------

EOF
    bdir=
    junkname=pure-junk-974adfkj38
    while [ x$bdir = x ]
    do
        # Ask the user (if not already set on the command-line).
        if [ x"$build_dir" = x ]; then
            if read -p"Please enter the top build directory: " build_dir; then
                just_a_place_holder_to_avoid_not_equal_test=1;
            else
                echo "ERROR: shell is in non-interactive-mode and no build directory specified."
                echo "The build directory (described above) is mandatory, configuration can't continue."
                echo "Please use '--build-dir' to specify a build directory non-interactively."
                exit 1
            fi
        fi

        # If it exists, see if we can write in it. If not, try making it.
        if [ -d $build_dir ]; then
            if mkdir $build_dir/$junkname 2> /dev/null; then
                instring="the already existing"
                bdir=$(absolute_dir $build_dir)
                rm -rf $build_dir/$junkname
            else
                echo " ** Can't write in '$build_dir'";
            fi
        else
            if mkdir $build_dir 2> /dev/null; then
                instring="the newly created"
                bdir=$(absolute_dir $build_dir)
            else
                echo " ** Can't create '$build_dir'";
            fi
        fi

        # If its given, make sure it isn't a subdirectory of the source
        # directory.
        if ! [ x"$bdir" = x ]; then
            if echo "$bdir/" \
                    | grep '^'$currentdir 2> /dev/null > /dev/null; then

                # If it was newly created, it will be empty, so delete it.
                if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi

                # Inform the user that this is not acceptable and reset `bdir'.
                bdir=
                echo " ** The build-directory cannot be under the source-directory."
            fi
        fi

	# If everything is fine until now, see if we're able to manipulate
	# file permissions.
	if ! [ x"$bdir" = x ]; then
            if ! $(check_permission $bdir); then
                # Unable to handle permissions well
                bdir=
                echo " ** File permissions can't be modified in this directory"
            else
                # Able to handle permissions, now check for 5GB free space
                # in the given partition (note that the number is in units
                # of 1024 bytes). If this is not the case, print a warning.
                if $(free_space_warning 5000000 $bdir); then
                    echo " !! LESS THAN 5GB FREE SPACE IN: $bdir"
                    echo " !! We recommend choosing another partition."
                    echo " !! Build will continue in 5 seconds..."
                    sleep 5
                fi
            fi
        fi

        # If the build directory was good, the loop will stop, if not,
        # reset `build_dir' to blank, so it continues asking for another
        # directory and let the user know that they must select a new
        # directory.
        if [ x$bdir = x ]; then
            build_dir=
            echo " ** Please select another directory."
            echo ""
        else
            echo " -- Build directory set to ($instring): '$bdir'"
        fi
    done
fi





# Input directory
# ---------------
if [ x"$input_dir" = x ]; then
    indir=$optionaldir
else
    indir=$input_dir
fi
noninteractive_sleep=2
if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
    cat <<EOF

----------------------------------
(OPTIONAL) Input dataset directory
----------------------------------

This project needs the dataset(s) listed in the following file:

      reproduce/analysis/config/INPUTS.conf

If you already have a copy of them on this system, please specify the
directory hosting them on this system. If they aren't present, they will be
downloaded automatically when necessary.

NOTE I: This directory is optional. If not given, or if the files can't be
found inside it, any necessary file will be downloaded directly in the
build directory and used.

NOTE II: If a directory is given, it will be used as read-only. Nothing
will be written into it, so no writing permissions are necessary.

TIP: If you have these files in multiple directories on your system and
don't want to make duplicates, you can create symbolic links to them and
put those symbolic links in the given top-level directory.

EOF
    # Read the input directory if interactive mode is enabled.
    if read -p"(OPTIONAL) Input datasets directory ($indir): " inindir; then
        just_a_place_holder_to_avoid_not_equal_test=1;
    else
        echo "WARNING: interactive-mode seems to be disabled!"
        echo "If you have a local copy of the inputs, use '--input-dir'."
        echo "... project configuration will continue in $noninteractive_sleep sec ..."
        sleep $noninteractive_sleep
    fi

    # In case an input-directory is given, write it in 'indir'.
    if [ x$inindir != x ]; then
        indir=$(absolute_dir $inindir)
        echo " -- Using '$indir'"
    fi
fi





# Dependency tarball directory
# ----------------------------
if [ x"$software_dir" = x ]; then
    ddir=$optionaldir
else
    ddir=$software_dir
fi
if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then
    cat <<EOF

---------------------------------------
(OPTIONAL) Software tarball directory
---------------------------------------

To ensure an identical build environment, the project will use its own
build of the programs it needs. Therefore the tarball of the relevant
programs are necessary.

If you don't specify any directory here, or it doesn't contain the tarball
of a dependency, it is necessary to have an internet connection because the
project will download the tarballs it needs automatically.

EOF
    # Read the software directory if interactive mode is enabled.
    if read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir; then
        just_a_place_holder_to_avoid_not_equal_test=1;
    else
        echo "WARNING: interactive-mode seems to be disabled!"
        echo "If you have a local copy of the software source, use '--software-dir'."
        echo "... project configuration will continue in $noninteractive_sleep sec ..."
        sleep $noninteractive_sleep
    fi

    # If given, write the software directory.
    if [ x"$tmpddir" != x ]; then
        ddir=$(absolute_dir $tmpddir)
        echo " -- Using '$ddir'"
    fi
fi





# Write the parameters into the local configuration file.
if [ $rewritepconfig = yes ]; then

    # Add commented notice.
    create_file_with_notice $pconf

    # Write the values.
    sed -e's|@bdir[@]|'"$bdir"'|' \
        -e's|@indir[@]|'"$indir"'|' \
        -e's|@ddir[@]|'"$ddir"'|' \
        -e's|@sys_cpath[@]|'"$sys_cpath"'|' \
        -e's|@downloader[@]|'"$downloader"'|' \
        -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
        $pconf.in >> $pconf
else
    # Read the values from existing configuration file.
    inbdir=$(awk '$1=="BDIR" {print $3}' $pconf)

    # Read the software directory.
    ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf)

    # The downloader command may contain multiple elements, so we'll just
    # change the (in memory) first and second tokens to empty space and
    # write the full line (the original file is unchanged).
    downloader=$(awk '$1=="DOWNLOADER" {$1=""; $2=""; print $0}' $pconf)

    # Make sure all necessary variables have a value
    err=0
    verr=0
    novalue=""
    if [ x"$inbdir"     = x ]; then novalue="BDIR, ";              fi
    if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER;  fi
    if [ x"$novalue"   != x ]; then verr=1; err=1;                 fi

    # Make sure `bdir' is an absolute path and it exists.
    berr=0
    ierr=0
    bdir=$(absolute_dir $inbdir)

    if ! [ -d $bdir  ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
    if [ $err = 1 ]; then
        cat <<EOF

#################################################################
########  ERORR reading existing configuration file  ############
#################################################################
EOF
        if [ $verr = 1 ]; then
            cat <<EOF

These variables have no value: $novalue.
EOF
        fi
        if [ $berr = 1 ]; then
           cat <<EOF

Couldn't create the build directory '$bdir' (value to 'BDIR') in
'$pconf'.
EOF
        fi

        cat <<EOF

Please run the configure script again (accepting to re-write existing
configuration file) so all the values can be filled and checked.
#################################################################
EOF
    fi
fi





# --------- Delete for no Gnuastro ---------
# Get the version of Gnuastro that must be used.
gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile)

# Gnuastro's local configuration settings
if [ $rewritegconfig = yes ]; then
    create_file_with_notice $glconf
    echo "# Minimum number of bytes to use HDD/SSD instead of RAM." >> $glconf
    echo " minmapsize $minmapsize"                                  >> $glconf
    echo                                                            >> $glconf
    echo "# Version of Gnuastro that must be used."                 >> $glconf
    echo " onlyversion $gversion"                                   >> $glconf
else
    ingversion=$(awk '$1=="onlyversion" {print $NF}' $glconf)
    if [ x$ingversion != x$gversion ]; then
           cat <<EOF
______________________________________________________
!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!

Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball
version that this project was designed to use in '$depverfile'
($gversion). Please re-run after removing the former file:

   $ rm $glconf
   $ ./project configure -e

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
        exit 1
    fi
fi
# ------------------------------------------





# Delete final configuration target
# ---------------------------------
#
# We only want to start running the project later if this script has
# completed successfully. To make sure it hasn't crashed in the middle
# (without the user noticing), in the end of this script we make a file and
# we'll delete it here (at the start). Therefore if the script crashed in
# the middle that file won't exist.
sdir=$bdir/software
finaltarget=$sdir/configuration-done.txt
if ! [ -d $sdir ];  then mkdir $sdir; fi
rm -f $finaltarget





# Project's top-level directories
# -------------------------------
#
# These directories are possibly needed by many steps of process, so to
# avoid too many directory dependencies throughout the software and
# analysis Makefiles (thus making them hard to read), we are just building
# them here
# Software tarballs
tardir=$sdir/tarballs
if ! [ -d $tardir ];  then mkdir $tardir; fi

# Installed software
instdir=$sdir/installed
if ! [ -d $instdir ]; then mkdir $instdir; fi

# To record software versions and citation.
verdir=$instdir/version-info
if ! [ -d $verdir ]; then mkdir $verdir; fi

# Program and library versions and citation.
ibidir=$verdir/proglib
if ! [ -d $ibidir ]; then mkdir $ibidir; fi

# Python module versions and citation.
ipydir=$verdir/python
if ! [ -d $ipydir ]; then mkdir $ipydir; fi

# Used software BibTeX entries.
ictdir=$verdir/cite
if ! [ -d $ictdir ]; then mkdir $ictdir; fi

# TeXLive versions.
itidir=$verdir/tex
if ! [ -d $itidir ]; then mkdir $itidir; fi

# Top-level LaTeX.
texdir=$bdir/tex
if ! [ -d $texdir ]; then mkdir $texdir; fi

# LaTeX macros.
mtexdir=$texdir/macros
if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi


# TeX build directory. If built in a group scenario, the TeX build
# directory must be separate for each member (so they can work on their
# relevant parts of the paper without conflicting with each other).
if [ "x$reproducible_paper_group_name" = x ]; then
    texbdir=$texdir/build
else
    user=$(whoami)
    texbdir=$texdir/build-$user
fi
if ! [ -d $texbdir ]; then mkdir $texbdir; fi

# TiKZ (for building figures within LaTeX).
tikzdir=$texbdir/tikz
if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi


# If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f' will delete
# them and we can continue. However, when the project is being built from
# the tarball, these two are not symbolic links but actual directories with
# the necessary built-components to build the PDF in them. In this case,
# because 'tex/build' is a directory, 'rm -f' will fail, so we'll just
# rename the two directories (as backup) and let the project build the
# proper symbolic links afterwards.
if rm -f tex/build; then
    rm -f tex/tikz
else
    mv tex/tikz tex/tikz-from-tarball
    mv tex/build tex/build-from-tarball
fi


# Set the symbolic links for easy access to the top project build
# directories. Note that these are put in each user's source/cloned
# directory, not in the build directory (which can be shared between many
# users and thus may already exist).
#
# Note: if we don't delete them first, it can happen that an extra link
# will be created in each directory that points to its parent. So to be
# safe, we are deleting all the links on each re-configure of the project.
rm -f .build .local .gnuastro
ln -s $bdir .build
ln -s $instdir .local
ln -s $texdir tex/build
ln -s $tikzdir tex/tikz
# --------- Delete for no Gnuastro ---------
ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
# ------------------------------------------


# Temporary software un-packing/build directory: if the host has the
# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
# today (>8GB) is large enough for the parallel building of the software.
#
# For the name of the directory under `/dev/shm' (for this project), we'll
# use the names of the two parent directories to the current/running
# directory, separated by a `-' instead of `/'. We'll then appended that
# with the user's name (in case multiple users may be working on similar
# project names). Maybe later, we can use something like `mktemp' to add
# random characters to this name and make it unique to every run (even for
# a single user).
tmpblddir=$sdir/build-tmp
rm -rf $tmpblddir/* $tmpblddir  # If its a link, we need to empty its
                                # contents first, then itself.

# Set the top-level shared memory location.
if [ -d /dev/shm ]; then     shmdir=/dev/shm
else                         shmdir=""
fi

# If a shared memory mounted directory exists and there is enough space
# there (in RAM), build a temporary directory for this project.
needed_space=2000000
if [ x"$shmdir" != x ]; then
    available_space=$(df $shmdir | awk 'NR==2{print $4}')
    if [ $available_space -gt $needed_space ]; then
        dirname=$(pwd | sed -e's/\// /g' \
                      | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
        tbshmdir=$shmdir/"$dirname"-$(whoami)
        if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
    fi
else
    tbshmdir=""
fi

# If a shared memory directory was created set `build-tmp' to be a
# symbolic link to it. Otherwise, just build the temporary build
# directory under the project build directory.
if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
else                        ln -s $tbshmdir $tmpblddir;
fi





# Inform the user that the build process is starting
# -------------------------------------------------
if [ $printnotice = yes ]; then
    tsec=10
    cat <<EOF

-------------------------
Building dependencies ...
-------------------------

Necessary dependency programs and libraries will be built in

  $sdir/installed

NOTE: the built software will NOT BE INSTALLED on your system (no root
access is required). They are only for local usage by this project.

**TIP**: you can see which software are being installed at every moment
with the following command. See "Inspecting status" section of
'README-hacking.md' for more. In short, run it while the project is being
configured (in another terminal, but in this same directory:
'$currentdir'):

  $ ./project --check-config

Project's configuration will continue in $tsec seconds.

-------------------------

EOF
    sleep $tsec
fi





# Number of threads to build software
# -----------------------------------
#
# If the user hasn't manually specified the number of threads, see if we
# can deduce it from the host:
#  - On systems with GNU Coreutils we have 'nproc'.
#  - On BSD-based systems (for example FreeBSD and macOS), we have a
#    'hw.ncpu' in the output of 'sysctl'.
#  - When none of the above work, just set the number of threads to 1.
if [ $jobs = 0 ]; then
    if type nproc > /dev/null 2> /dev/null; then
        numthreads=$(nproc --all);
    else
        numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}')
        if [ x"$numthreads" = x ]; then numthreads=1; fi
    fi
else
    numthreads=$jobs
fi




# Paths needed by the host compiler (only for `basic.mk')
# -------------------------------------------------------
#
# At the end of the basic build, we need to build GCC. But GCC will build
# in multiple phases, making its own simple compiler in order to build
# itself completely. The intermediate/simple compiler doesn't recognize
# some system specific locations like `/usr/lib/ARCHITECTURE' that some
# operating systems use. We thus need to tell the intermediate compiler
# where its necessary libraries and headers are.
if [ x"$sys_library_path" != x ]; then
    if [ x"$LIBRARY_PATH" = x ]; then
        export LIBRARY_PATH="$sys_library_path"
    else
        export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
    fi
    if [ x"$CPATH" = x ]; then
        export CPATH="$sys_cpath"
    else
        export CPATH="$CPATH:$sys_cpath"
    fi
fi





# Find Zenodo URL for software downloading
# ----------------------------------------
#
# All free-software source tarballs that are potentially used in Maneage
# are also archived in Zenodo with a certain concept-DOI. A concept-DOI is
# a Zenodo terminology, meaning a fixed DOI of the project (that can have
# many sub-DOIs for different versions). By default, the concept-DOI points
# to the most recently uploaded version. However, the concept-DOI itself is
# not directly usable for downloading files. The concept-DOI will just take
# us to the top webpage of the most recent version of the upload.
#
# The problem is that as more software are added (as new Zenodo versions),
# the most recent Zenodo-URL that the concept-DOI points to, also
# changes. The most reliable solution was found to be the tiny script below
# which will download the DOI-resolved webpage, and extract the Zenodo-URL
# of the most recent version from there (using the 'coreutils' tarball as
# an example, the directory part of the URL for all the other software are
# the same).
user_backup_urls=""
zenodocheck=.build/software/zenodo-check.html
if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then
    zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \
                    | sed -n -e'/http/p' \
                    | tr ' ' '\n' \
                    | grep http \
                    | sed -e 's/href="//' -e 's|/coreutils| |' \
                    | awk 'NR==1{print $1}')
else
    zenodourl=""
fi
rm -f $zenodocheck

# Add the Zenodo URL to the user's given back software URLs. Since the user
# can specify 'user_backup_urls' (not yet implemented as an option in
# './project'), we'll give preference to their specified servers, then add
# the Zenodo URL afterwards.
user_backup_urls="$user_backup_urls $zenodourl"





# Build core tools for project
# ----------------------------
#
# Here we build the core tools that 'basic.mk' depends on: Lzip
# (compression program), GNU Make (that 'basic.mk' is written in), Dash
# (minimal Bash-like shell) and Flock (to lock files and enable serial
# download).
./reproduce/software/shell/pre-make-build.sh \
    "$bdir" "$ddir" "$downloader" "$user_backup_urls"





# Build other basic tools our own GNU Make
# ----------------------------------------
#
# When building these software we don't have our own un-packing software,
# Bash, Make, or AWK. In this step, we'll install such low-level basic
# tools, but we have to be very portable (and use minimal features in all).
echo; echo "Building necessary software (if necessary)..."
.local/bin/make -k -f reproduce/software/make/basic.mk \
     user_backup_urls="$user_backup_urls" \
     sys_library_path=$sys_library_path \
     rpath_command=$rpath_command \
     static_build=$static_build \
     numthreads=$numthreads \
     needs_ldl=$needs_ldl \
     on_mac_os=$on_mac_os \
     host_cc=$host_cc \
     -j$numthreads





# All other software
# ------------------
#
# We will be making all the dependencies before running the top-level
# Makefile. To make the job easier, we'll do it in a Makefile, not a
# script. Bash and Make were the tools we need to run Makefiles, so we had
# to build them in this script. But after this, we can rely on Makefiles.
if [ $jobs = 0 ]; then
    numthreads=$(.local/bin/nproc --all)
else
    numthreads=$jobs
fi
.local/bin/env -i HOME=$bdir \
     .local/bin/make -k -f reproduce/software/make/high-level.mk \
          user_backup_urls="$user_backup_urls" \
          sys_library_path=$sys_library_path \
          rpath_command=$rpath_command \
          all_highlevel=$all_highlevel \
          static_build=$static_build \
          numthreads=$numthreads \
          on_mac_os=$on_mac_os \
          sys_cpath=$sys_cpath \
          host_cc=$host_cc \
          -j$numthreads





# Make sure TeX Live installed successfully
# -----------------------------------------
#
# TeX Live is managed over the internet, so if there isn't any, or it
# suddenly gets cut, it can't be built. However, when TeX Live isn't
# installed, the project can do all its processing independent of it. It
# will just stop at the stage when all the processing is complete and it is
# only necessary to build the PDF.  So we don't want to stop the project's
# configuration and building if its not present.
if [ -f $itidir/texlive-ready-tlmgr ]; then
    texlive_result=$(cat $itidir/texlive-ready-tlmgr)
else
    texlive_result="NOT!"
fi
if [ x"$texlive_result" = x"NOT!" ]; then
    cat <<EOF

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

TeX Live couldn't be installed during the configuration (probably because
there were downloading problems). TeX Live is only necessary in making the
final PDF (which is only done after all the analysis has been complete). It
is not used at all during the analysis.

Therefore, if you don't need the final PDF, and just want to do the
analysis, you can safely ignore this warning and continue.

If you later have internet access and would like to add TeX live to your
project, please delete the respective files, then re-run configure as shown
below.

    rm .local/version-info/tex/texlive-ready-tlmgr
    ./project configure -e

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

EOF
fi





# Citation of installed software
#
# After everything is installed, we'll put all the names and versions in a
# human-readable paragraph and also prepare the BibTeX citation for the
# software.
prepare_name_version ()
{
    # First see if the (possible) `*' in the input arguments corresponds to
    # anything. Note that some of the given directories may be empty (no
    # software installed).
    hasfiles=0
    for f in $@; do
        if [ -f $f ]; then hasfiles=1; break; fi;
    done

    # If there are any files, merge all the names in a paragraph.
    if [ $hasfiles = 1 ]; then

        # Count how many names there are. This is necessary to identify the
        # last element.
        num=$(.local/bin/cat $@ \
                  | .local/bin/sed '/^\s*$/d' \
                  | .local/bin/wc -l)

        # Put them all in one paragraph, while sorting them, commenting any
        # possible underscores and removing blank lines.
        .local/bin/cat $@ \
            | .local/bin/sort \
            | .local/bin/sed -e's|_|\\_|' \
            | .local/bin/awk 'NF>0 { \
                  c++; \
                  if(c==1) \
                    { \
                      if('$num'==1) printf("%s", $0); \
                      else          printf("%s", $0); \
                    } \
                  else if(c=='$num') printf(" and %s\n", $0); \
                  else printf(", %s", $0) \
                }'
    fi
}

# Import the context/sentences for placing between the list of software
# names during their acknowledgment.
. $cdir/software_acknowledge_context.sh

# Report the different software in separate contexts (separating Python and
# TeX packages from the C/C++ programs and libraries).
proglibs=$(prepare_name_version $verdir/proglib/*)
pymodules=$(prepare_name_version $verdir/python/*)
texpkg=$(prepare_name_version $verdir/tex/texlive)

# Acknowledge these software packages in a LaTeX paragraph.
pkgver=$mtexdir/dependencies.tex

# Add the text to the ${pkgver} file.
.local/bin/echo "$thank_software_introduce " > $pkgver
.local/bin/echo "$thank_progs_libs $proglibs. "   >> $pkgver
if [ x"$pymodules" != x ]; then
    .local/bin/echo "$thank_python $pymodules. "   >> $pkgver
fi
.local/bin/echo "$thank_latex $texpkg. " >> $pkgver
.local/bin/echo "$thank_software_conclude" >> $pkgver

# Prepare the BibTeX entries for the used software (if there are any).
hasentry=0
bibfiles="$ictdir/*"
for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done;

# Make sure we start with an empty output file.
pkgbib=$mtexdir/dependencies-bib.tex
echo "" > $pkgbib

# Fill it in with all the BibTeX entries in this directory. We'll just
# avoid writing any comments (usually copyright notices) and also put an
# empty line after each file's contents to make the output more readable.
if [ $hasentry = 1 ]; then
    for f in $bibfiles; do
        awk '!/^%/{print} END{print ""}' $f >> $pkgbib
    done
fi





# Clean the temporary build directory
# ---------------------------------
#
# By the time the script reaches here the temporary software build
# directory should be empty, so just delete it. Note `tmpblddir' may be a
# symbolic link to shared memory. So, to work in any scenario, first delete
# the contents of the directory (if it has any), then delete `tmpblddir'.
.local/bin/rm -rf $tmpblddir/* $tmpblddir





# Register successful completion
# ------------------------------
echo `.local/bin/date` > $finaltarget






# Final notice
# ------------
#
# The configuration is now complete, we can inform the user on the next
# step(s) to take.
if [ x$reproducible_paper_group_name = x ]; then
    buildcommand="./project make -j8"
else
    buildcommand="./project make --group=$reproducible_paper_group_name -j8"
fi
cat <<EOF

----------------
The project and its environment are configured with no errors.

To change the configuration later, you can re-run './project configure' or
manually edit 'reproduce/software/config/LOCAL.conf'. Just be careful with
the build-directory: its location is hard-coded in the installed software
so if you change it manually, many of the project's software will crash. If
you have to use another built-directory, just re-configure a clean project
there.

Please run the following command to start the project.
(Replace '8' with the number of CPU threads on your system)

    $buildcommand

EOF