Error in re-building vignettes:
  ...
Loading required package: Rcpp

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Compiling model
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=result) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

the number of chains is less than 1; sampling not done
Saving compiled model to /tmp/RtmpZlkUyP/DeLorean-exact-sizes.rds
TSP:scaled:none:1; time=2.25999999999999s; LL=-3337.95001463371
R2E:scaled:none:1; time=2.27000000000001s; LL=-3312.19003094297
HC:scaled:none:1; time=0.00499999999999545s; LL=-3368.38279704188
GW:scaled:none:1; time=0.007000000000005s; LL=-3303.85068991529
OLO:scaled:none:1; time=0.00499999999999545s; LL=-3300.07998740641
R2E:unscaled:none:1; time=0.00800000000000978s; LL=-3314.97859256684
TSP:unscaled:none:1; time=0.0120000000000005s; LL=-3301.47808530183
GW:unscaled:none:1; time=0.0190000000000055s; LL=-3306.56560831851
HC:unscaled:none:1; time=0.0040000000000191s; LL=-3444.20380317136
OLO:unscaled:none:1; time=0.00499999999999545s; LL=-3305.98364627545
TSP:scaled:pca:1; time=0.0109999999999957s; LL=-3493.89219277604
R2E:scaled:pca:1; time=0.0120000000000005s; LL=-3441.0657383941
HC:scaled:pca:1; time=0.0040000000000191s; LL=-3482.06632126203
OLO:scaled:pca:1; time=0.00399999999999068s; LL=-3454.52140805557
GW:scaled:pca:1; time=0.00499999999999545s; LL=-3454.52140805557
R2E:unscaled:pca:1; time=0.0109999999999957s; LL=-3535.55073235236
TSP:unscaled:pca:1; time=0.00900000000001455s; LL=-3430.09084316101
GW:unscaled:pca:1; time=0.00499999999999545s; LL=-3423.77760024302
HC:unscaled:pca:1; time=0.00500000000002387s; LL=-3497.09853061289
TSP:scaled:ica:1; time=0.0169999999999959s; LL=-3441.0657383941
OLO:unscaled:pca:1; time=0.00499999999999545s; LL=-3423.77760024302
HC:scaled:ica:1; time=0.00500000000002387s; LL=-3482.06632126203
R2E:scaled:ica:1; time=0.0190000000000055s; LL=-3441.0657383941
OLO:scaled:ica:1; time=0.00499999999999545s; LL=-3454.52140805557
GW:scaled:ica:1; time=0.00600000000000023s; LL=-3454.52140805557
R2E:unscaled:ica:1; time=0.0100000000000193s; LL=-3535.55073235236
TSP:unscaled:ica:1; time=0.0109999999999957s; LL=-3414.81658041188
GW:unscaled:ica:1; time=0.0190000000000055s; LL=-3423.77760024302
HC:unscaled:ica:1; time=0.00500000000002387s; LL=-3497.09853061289
TSP:scaled:mds:1; time=0.0100000000000193s; LL=-3441.0657383941
OLO:unscaled:ica:1; time=0.00399999999999068s; LL=-3423.77760024302
HC:scaled:mds:1; time=0.00399999999999068s; LL=-3482.06632126203
R2E:scaled:mds:1; time=0.0120000000000005s; LL=-3441.0657383941
OLO:scaled:mds:1; time=0.00499999999999545s; LL=-3454.52140805557
GW:scaled:mds:1; time=0.00499999999999545s; LL=-3454.52140805557
R2E:unscaled:mds:1; time=0.00999999999999091s; LL=-3535.55073235236
TSP:unscaled:mds:1; time=0.00799999999998136s; LL=-3423.77760024302
GW:unscaled:mds:1; time=0.00500000000002387s; LL=-3423.77760024302
HC:unscaled:mds:1; time=0.00399999999999068s; LL=-3497.09853061289
TSP:scaled:pca:2; time=0.0109999999999957s; LL=-3331.43067250236
OLO:unscaled:mds:1; time=0.00499999999999545s; LL=-3423.77760024302
HC:scaled:pca:2; time=0.00499999999999545s; LL=-3483.40649497136
R2E:scaled:pca:2; time=0.0109999999999957s; LL=-3347.95299236194
OLO:scaled:pca:2; time=0.00499999999999545s; LL=-3344.78375661556
GW:scaled:pca:2; time=0.00499999999999545s; LL=-3419.93511374737
TSP:unscaled:pca:2; time=0.00999999999999091s; LL=-3324.58621656222
R2E:unscaled:pca:2; time=0.0229999999999961s; LL=-3328.4926673327
HC:unscaled:pca:2; time=0.00499999999999545s; LL=-3503.28326952046
GW:unscaled:pca:2; time=0.00500000000002387s; LL=-3309.19258134348
OLO:unscaled:pca:2; time=0.00399999999999068s; LL=-3315.41529111282
TSP:scaled:kfa:2; time=0.0340000000000202s; LL=-3486.84174565715
HC:scaled:kfa:2; time=0.00399999999999068s; LL=-3534.23969667457
R2E:scaled:kfa:2; time=0.0349999999999966s; LL=-3420.58481180895
GW:scaled:kfa:2; time=0.00499999999999545s; LL=-3353.97801746589
OLO:scaled:kfa:2; time=0.00500000000002387s; LL=-3438.36328456982
TSP:unscaled:kfa:2; time=0.0270000000000152s; LL=-3405.93651637468
R2E:unscaled:kfa:2; time=0.0270000000000152s; LL=-3507.65121829661
HC:unscaled:kfa:2; time=0.00499999999999545s; LL=-3509.15724964732
GW:unscaled:kfa:2; time=0.00499999999999545s; LL=-3423.00562389161
OLO:unscaled:kfa:2; time=0.00500000000002387s; LL=-3425.27182950106
TSP:scaled:ica:2; time=0.0120000000000005s; LL=-3350.48319969101
R2E:scaled:ica:2; time=0.0130000000000052s; LL=-3425.25261742118
HC:scaled:ica:2; time=0.00399999999999068s; LL=-3466.20727625058
GW:scaled:ica:2; time=0.00499999999999545s; LL=-3402.07773271805
OLO:scaled:ica:2; time=0.00500000000002387s; LL=-3323.606537308
TSP:unscaled:ica:2; time=0.0109999999999957s; LL=-3319.89473701415
R2E:unscaled:ica:2; time=0.0129999999999768s; LL=-3385.33003508959
HC:unscaled:ica:2; time=0.0040000000000191s; LL=-3482.57983520352
GW:unscaled:ica:2; time=0.00900000000001455s; LL=-3411.95344834032
OLO:unscaled:ica:2; time=0.00499999999999545s; LL=-3307.61071434979
TSP:scaled:mds:2; time=0.00999999999999091s; LL=-3342.49562108782
R2E:scaled:mds:2; time=0.0109999999999957s; LL=-3345.2414701583
HC:scaled:mds:2; time=0.0169999999999959s; LL=-3483.40649497136
GW:scaled:mds:2; time=0.00499999999999545s; LL=-3419.93511374737
OLO:scaled:mds:2; time=0.00399999999999068s; LL=-3344.78375661556
TSP:unscaled:mds:2; time=0.00900000000001455s; LL=-3317.13436877952
R2E:unscaled:mds:2; time=0.0100000000000193s; LL=-3328.4926673327
HC:unscaled:mds:2; time=0.0040000000000191s; LL=-3503.28326952046
GW:unscaled:mds:2; time=0.00600000000000023s; LL=-3309.19258134348
OLO:unscaled:mds:2; time=0.0040000000000191s; LL=-3315.41529111282
TSP:scaled:pca:4; time=0.0100000000000193s; LL=-3303.61638234433
R2E:scaled:pca:4; time=0.0180000000000007s; LL=-3301.9118654004
HC:scaled:pca:4; time=0.0040000000000191s; LL=-3424.94267889229
OLO:scaled:pca:4; time=0.00399999999999068s; LL=-3299.21628045383
GW:scaled:pca:4; time=0.00499999999999545s; LL=-3348.29987539985
R2E:unscaled:pca:4; time=0.0100000000000193s; LL=-3313.88438164518
TSP:unscaled:pca:4; time=0.0219999999999914s; LL=-3306.06076853946
GW:unscaled:pca:4; time=0.007000000000005s; LL=-3303.42211241529
HC:unscaled:pca:4; time=0.00399999999999068s; LL=-3439.19527733066
TSP:scaled:kfa:4; time=0.0270000000000152s; LL=-3354.14424644908
OLO:unscaled:pca:4; time=0.00499999999999545s; LL=-3301.00820515642
HC:scaled:kfa:4; time=0.0040000000000191s; LL=-3461.40431175951
R2E:scaled:kfa:4; time=0.0420000000000016s; LL=-3461.15491893835
OLO:scaled:kfa:4; time=0.00500000000002387s; LL=-3355.14535839129
GW:scaled:kfa:4; time=0.00499999999999545s; LL=-3344.26810154656
R2E:unscaled:kfa:4; time=0.0289999999999964s; LL=-3532.89998159563
TSP:unscaled:kfa:4; time=0.0240000000000009s; LL=-3395.25040696016
GW:unscaled:kfa:4; time=0.00499999999999545s; LL=-3437.01773755577
HC:unscaled:kfa:4; time=0.0040000000000191s; LL=-3465.8208841795
TSP:scaled:ica:4; time=0.0180000000000007s; LL=-3373.77625003047
OLO:unscaled:kfa:4; time=0.00399999999999068s; LL=-3389.3648934463
HC:scaled:ica:4; time=0.00499999999999545s; LL=-3497.61465742304
OLO:scaled:ica:4; time=0.00499999999999545s; LL=-3367.60856144608
R2E:scaled:ica:4; time=0.0269999999999868s; LL=-3401.31917572177
GW:scaled:ica:4; time=0.00499999999999545s; LL=-3372.38638995931
R2E:unscaled:ica:4; time=0.114000000000004s; LL=-3435.57413658386
GW:unscaled:ica:4; time=0.00499999999999545s; LL=-3556.06488716102
TSP:unscaled:ica:4; time=0.0160000000000196s; LL=-3442.98558010387
TSP:scaled:mds:4; time=0.00899999999998613s; LL=-3308.01150295391
HC:unscaled:ica:4; time=0.00399999999999068s; LL=-3569.93698361197
HC:scaled:mds:4; time=0.00499999999999545s; LL=-3424.94267889229
OLO:unscaled:ica:4; time=0.0040000000000191s; LL=-3440.37866973067
OLO:scaled:mds:4; time=0.00499999999999545s; LL=-3299.21628045383
R2E:scaled:mds:4; time=0.0120000000000005s; LL=-3301.9118654004
R2E:unscaled:mds:4; time=0.0190000000000055s; LL=-3313.88438164518
GW:scaled:mds:4; time=0.00800000000000978s; LL=-3348.29987539985
GW:unscaled:mds:4; time=0.00499999999999545s; LL=-3303.42211241529
TSP:unscaled:mds:4; time=0.00900000000001455s; LL=-3306.06076853946
TSP:scaled:pca:8; time=0.00899999999998613s; LL=-3335.86590567257
HC:unscaled:mds:4; time=0.0120000000000005s; LL=-3439.19527733066
HC:scaled:pca:8; time=0.0040000000000191s; LL=-3410.67230732234
OLO:unscaled:mds:4; time=0.00600000000000023s; LL=-3301.00820515642
OLO:scaled:pca:8; time=0.00399999999999068s; LL=-3296.01814550528
R2E:scaled:pca:8; time=0.0109999999999957s; LL=-3303.49379273087
R2E:unscaled:pca:8; time=0.0109999999999957s; LL=-3316.32462898471
GW:scaled:pca:8; time=0.00600000000000023s; LL=-3304.59741713766
GW:unscaled:pca:8; time=0.00499999999999545s; LL=-3317.02287829198
TSP:unscaled:pca:8; time=0.0240000000000009s; LL=-3322.6067949875
TSP:scaled:kfa:8; time=0.0360000000000014s; LL=-3332.50070627217
HC:unscaled:pca:8; time=0.00500000000002387s; LL=-3447.45179885413
HC:scaled:kfa:8; time=0.00500000000002387s; LL=-3404.32934093838
OLO:unscaled:pca:8; time=0.00399999999999068s; LL=-3305.88045667667
OLO:scaled:kfa:8; time=0.00499999999999545s; LL=-3316.03309283331
R2E:scaled:kfa:8; time=0.0380000000000109s; LL=-3442.25057023245
R2E:unscaled:kfa:8; time=0.0339999999999918s; LL=-3457.68670314948
GW:scaled:kfa:8; time=0.00500000000002387s; LL=-3362.09898096891
GW:unscaled:kfa:8; time=0.00500000000002387s; LL=-3315.36012889576
TSP:unscaled:kfa:8; time=0.0349999999999966s; LL=-3359.03936437827
HC:unscaled:kfa:8; time=0.00399999999999068s; LL=-3393.63605882866
TSP:scaled:ica:8; time=0.129999999999995s; LL=-3425.32617397879
OLO:unscaled:kfa:8; time=0.00399999999999068s; LL=-3329.54744474637
HC:scaled:ica:8; time=0.00499999999999545s; LL=-3412.99377456701
OLO:scaled:ica:8; time=0.00499999999999545s; LL=-3420.95057605883
R2E:scaled:ica:8; time=0.11099999999999s; LL=-3647.38139016248
GW:scaled:ica:8; time=0.00500000000002387s; LL=-3420.1826218935
R2E:unscaled:ica:8; time=0.112000000000023s; LL=-3604.33961483319
GW:unscaled:ica:8; time=0.00499999999999545s; LL=-3498.82244952718
TSP:unscaled:ica:8; time=0.106999999999999s; LL=-3410.62126971358
TSP:scaled:mds:8; time=0.00999999999999091s; LL=-3306.74755101413
HC:unscaled:ica:8; time=0.0180000000000007s; LL=-3538.61667195513
HC:scaled:mds:8; time=0.00399999999999068s; LL=-3410.67230732234
OLO:unscaled:ica:8; time=0.00399999999999068s; LL=-3407.48090953781
OLO:scaled:mds:8; time=0.00500000000002387s; LL=-3296.01814550528
R2E:scaled:mds:8; time=0.0120000000000005s; LL=-3318.8359242044
R2E:unscaled:mds:8; time=0.0100000000000193s; LL=-3316.32462898471
GW:scaled:mds:8; time=0.00499999999999545s; LL=-3304.59741713766
GW:unscaled:mds:8; time=0.007000000000005s; LL=-3317.02287829198
TSP:unscaled:mds:8; time=0.00900000000001455s; LL=-3303.77813158253
HC:unscaled:mds:8; time=0.00499999999999545s; LL=-3447.45179885413
OLO:unscaled:mds:8; time=0.00600000000000023s; LL=-3305.88045667667
Using ordering OLO:scaled:pca:8; LL=-3296.01814550528
Using ordering OLO:scaled:pca:4; LL=-3299.21628045383
Joining, by = "c"
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:1:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Core:531:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:2:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/LU:47:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Cholesky:12:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Jacobi:29:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Cholesky:43:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:4:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/QR:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Householder:27:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:5:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/SVD:48:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:6:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Geometry:58:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Dense:7:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Eigenvalues:58:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Sparse:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/SparseCore:66:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Sparse:27:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/OrderingMethods:71:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Sparse:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/SparseCholesky:43:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Sparse:32:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/SparseQR:35:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/Sparse:33:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:32:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/CholmodSupport:45:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:35:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:39:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:3:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/RcppEigenForward.h:40:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:309:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/prob/multinomial_rng.hpp:10:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/scal/prob/binomial_rng.hpp:10:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/random/binomial_distribution.hpp:407:9: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
        struct {
        ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/heterogeneous_system.hpp:34:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/dimension.hpp:21:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/dimension.hpp:21:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/dimension_list.hpp:131:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/heterogeneous_system.hpp:39:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/linear_algebra.hpp:20:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/heterogeneous_system.hpp:40:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/unscale.hpp:28:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:20:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/detail/conversion_impl.hpp:21:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:44:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/typeof/typeof.hpp:196:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP'
     <boost/typeof/incr_registration_group.hpp>
            ^
In file included from file5c945fece1db.cpp:8:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math.hpp:4:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat.hpp:325:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/arr.hpp:49:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/scal.hpp:316:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/scal/prob/neg_binomial_2_ccdf_log.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/scal/prob/neg_binomial_2_lccdf.hpp:11:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/scal/prob/neg_binomial_ccdf_log.hpp:5:
In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/scal/prob/neg_binomial_lccdf.hpp:24:
In file included from /tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/random/negative_binomial_distribution.hpp:21:
/tmp/RtmpSHtL91/RLIBS_158a6877a506/BH/include/boost/random/poisson_distribution.hpp:338:9: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
        struct {
        ^
file5c945fece1db.cpp:223:1: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
matrix_d
^~~~~~~~
stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:224:21: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
cov_symmetric(const row_vector_d& tau,
                    ^~~~~~~~~~~~
                    stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:272:9: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
        matrix_d
        ^~~~~~~~
        stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:273:22: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
    operator()(const row_vector_d& tau,
                     ^~~~~~~~~~~~
                     stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:281:1: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
matrix_d
^~~~~~~~
stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:282:11: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
cov(const row_vector_d& tau1,
          ^~~~~~~~~~~~
          stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:283:15: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
        const row_vector_d& tau2,
              ^~~~~~~~~~~~
              stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:325:9: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
        matrix_d
        ^~~~~~~~
        stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:326:22: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
    operator()(const row_vector_d& tau1,
                     ^~~~~~~~~~~~
                     stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:327:15: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
        const row_vector_d& tau2,
              ^~~~~~~~~~~~
              stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:336:30: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
pretty_print_tri_lower(const matrix_d& x) {
                             ^~~~~~~~
                             stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:386:22: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
    operator()(const matrix_d& x, std::ostream* pstream__ = &Rcpp::Rcout) const {
                     ^~~~~~~~
                     stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:456:1: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
matrix_d cov_symmetric(const row_vector_d& tau, const int& periodic, const double& period, const double& l);
^~~~~~~~
stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:456:30: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
matrix_d cov_symmetric(const row_vector_d& tau, const int& periodic, const double& period, const double& l);
                             ^~~~~~~~~~~~
                             stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:461:42: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
    Rcpp::traits::input_parameter< const row_vector_d& >::type tau(tauSEXP);
                                         ^~~~~~~~~~~~
                                         stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:470:1: error: unknown type name 'matrix_d'; did you mean 'stan::math::matrix_d'?
matrix_d cov(const row_vector_d& tau1, const row_vector_d& tau2, const int& periodic, const double& period, const double& l);
^~~~~~~~
stan::math::matrix_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:19:63: note: 'stan::math::matrix_d' declared here
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic> matrix_d;
                                                              ^
file5c945fece1db.cpp:470:20: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
matrix_d cov(const row_vector_d& tau1, const row_vector_d& tau2, const int& periodic, const double& period, const double& l);
                   ^~~~~~~~~~~~
                   stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:470:46: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
matrix_d cov(const row_vector_d& tau1, const row_vector_d& tau2, const int& periodic, const double& period, const double& l);
                                             ^~~~~~~~~~~~
                                             stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
file5c945fece1db.cpp:475:42: error: unknown type name 'row_vector_d'; did you mean 'stan::math::row_vector_d'?
    Rcpp::traits::input_parameter< const row_vector_d& >::type tau1(tau1SEXP);
                                         ^~~~~~~~~~~~
                                         stan::math::row_vector_d
/data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/mat/fun/typedefs.hpp:29:50: note: 'stan::math::row_vector_d' declared here
typedef Eigen::Matrix<double, 1, Eigen::Dynamic> row_vector_d;
                                                 ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
27 warnings and 20 errors generated.
make[1]: *** [/data/gannet/ripley/R/R-clang/etc/Makeconf:166: file5c945fece1db.o] Error 1
Quitting from lines 145-146 (DeLorean.Rmd) 
Here is the C++ code that does not compile. Please report bug.
Error: processing vignette 'DeLorean.Rmd' failed with diagnostics:
Error 1 occurred building shared library.
Execution halted