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/RtmphQF0pb/DeLorean-exact-sizes.rds
R2E:scaled:none:1; time=1.13800000000001s; LL=-3338.07896522891
TSP:scaled:none:1; time=1.20699999999999s; LL=-3310.91038570985
GW:scaled:none:1; time=0.0169999999999959s; LL=-3346.49537619061
HC:scaled:none:1; time=0.00300000000000011s; LL=-3484.34094758831
TSP:unscaled:none:1; time=0.007000000000005s; LL=-3291.46182858414
OLO:scaled:none:1; time=0.00300000000000011s; LL=-3297.72049007404
HC:unscaled:none:1; time=0.00199999999999534s; LL=-3374.20722103277
R2E:unscaled:none:1; time=0.00500000000000966s; LL=-3324.5290231375
OLO:unscaled:none:1; time=0.00300000000000011s; LL=-3300.01815416152
GW:unscaled:none:1; time=0.00300000000000011s; LL=-3305.48760073288
R2E:scaled:pca:1; time=0.007000000000005s; LL=-3474.87917497478
TSP:scaled:pca:1; time=0.00600000000000023s; LL=-3435.57162702986
GW:scaled:pca:1; time=0.00300000000000011s; LL=-3388.09234610165
HC:scaled:pca:1; time=0.00199999999999534s; LL=-3481.35241069254
TSP:unscaled:pca:1; time=0.00499999999999545s; LL=-3362.10974153015
OLO:scaled:pca:1; time=0.00199999999999534s; LL=-3388.09234610165
HC:unscaled:pca:1; time=0.00300000000000011s; LL=-3503.44676899423
R2E:unscaled:pca:1; time=0.00600000000000023s; LL=-3362.10974153015
OLO:unscaled:pca:1; time=0.00300000000000011s; LL=-3362.10974153015
GW:unscaled:pca:1; time=0.00300000000000011s; LL=-3362.10974153015
R2E:scaled:ica:1; time=0.0240000000000009s; LL=-3474.87917497478
TSP:scaled:ica:1; time=0.0100000000000051s; LL=-3474.87917497478
HC:scaled:ica:1; time=0.00300000000000011s; LL=-3481.35241069254
GW:scaled:ica:1; time=0.00300000000000011s; LL=-3388.09234610165
OLO:scaled:ica:1; time=0.00300000000000011s; LL=-3388.09234610165
TSP:unscaled:ica:1; time=0.00600000000000023s; LL=-3362.10974153015
R2E:unscaled:ica:1; time=0.00600000000000023s; LL=-3362.10974153015
HC:unscaled:ica:1; time=0.00199999999999534s; LL=-3503.44676899423
GW:unscaled:ica:1; time=0.00300000000000011s; LL=-3362.10974153015
OLO:unscaled:ica:1; time=0.00300000000000011s; LL=-3362.10974153015
TSP:scaled:mds:1; time=0.0100000000000051s; LL=-3474.87917497478
R2E:scaled:mds:1; time=0.00600000000000023s; LL=-3474.87917497478
HC:scaled:mds:1; time=0.00300000000000011s; LL=-3481.35241069254
GW:scaled:mds:1; time=0.00300000000000011s; LL=-3388.09234610165
OLO:scaled:mds:1; time=0.00199999999999534s; LL=-3388.09234610165
TSP:unscaled:mds:1; time=0.00499999999999545s; LL=-3348.29158092303
R2E:unscaled:mds:1; time=0.00499999999999545s; LL=-3362.10974153015
HC:unscaled:mds:1; time=0.00300000000000011s; LL=-3503.44676899423
GW:unscaled:mds:1; time=0.00300000000000011s; LL=-3362.10974153015
OLO:unscaled:mds:1; time=0.00300000000000011s; LL=-3362.10974153015
TSP:scaled:pca:2; time=0.00499999999999545s; LL=-3332.83495805864
R2E:scaled:pca:2; time=0.00600000000000023s; LL=-3444.38361439832
HC:scaled:pca:2; time=0.00199999999999534s; LL=-3493.44472088626
GW:scaled:pca:2; time=0.00300000000000011s; LL=-3444.03854676453
OLO:scaled:pca:2; time=0.00300000000000011s; LL=-3362.83441011363
TSP:unscaled:pca:2; time=0.00499999999999545s; LL=-3330.38148636013
R2E:unscaled:pca:2; time=0.00600000000000023s; LL=-3342.71043821784
HC:unscaled:pca:2; time=0.00300000000000011s; LL=-3486.62451825951
GW:unscaled:pca:2; time=0.00300000000000011s; LL=-3344.55965382229
OLO:unscaled:pca:2; time=0.00200000000000955s; LL=-3335.58320239201
TSP:scaled:kfa:2; time=0.0160000000000053s; LL=-3508.70911231924
R2E:scaled:kfa:2; time=0.0180000000000007s; LL=-3486.46458031989
HC:scaled:kfa:2; time=0.00200000000000955s; LL=-3569.22848578703
GW:scaled:kfa:2; time=0.00300000000000011s; LL=-3414.73814415514
OLO:scaled:kfa:2; time=0.00199999999999534s; LL=-3493.25436497566
TSP:unscaled:kfa:2; time=0.0120000000000005s; LL=-3443.58250887778
R2E:unscaled:kfa:2; time=0.012999999999991s; LL=-3423.16613990411
HC:unscaled:kfa:2; time=0.00199999999999534s; LL=-3486.4590165078
GW:unscaled:kfa:2; time=0.00300000000000011s; LL=-3402.41304604355
OLO:unscaled:kfa:2; time=0.00199999999999534s; LL=-3402.07484906091
TSP:scaled:ica:2; time=0.00699999999999079s; LL=-3355.59290890861
R2E:scaled:ica:2; time=0.007000000000005s; LL=-3483.7857430921
HC:scaled:ica:2; time=0.00200000000000955s; LL=-3507.34238453862
GW:scaled:ica:2; time=0.00300000000000011s; LL=-3438.0300640229
OLO:scaled:ica:2; time=0.00199999999999534s; LL=-3338.4473967603
TSP:unscaled:ica:2; time=0.007000000000005s; LL=-3341.87415988776
R2E:unscaled:ica:2; time=0.00699999999999079s; LL=-3451.05379150953
HC:unscaled:ica:2; time=0.00199999999999534s; LL=-3467.11926578367
GW:unscaled:ica:2; time=0.00199999999999534s; LL=-3432.00541725615
OLO:unscaled:ica:2; time=0.00199999999999534s; LL=-3338.13162829926
TSP:scaled:mds:2; time=0.00499999999999545s; LL=-3329.51425552743
R2E:scaled:mds:2; time=0.00699999999999079s; LL=-3444.38361439832
HC:scaled:mds:2; time=0.00200000000000955s; LL=-3493.44472088626
GW:scaled:mds:2; time=0.00300000000000011s; LL=-3444.03854676453
OLO:scaled:mds:2; time=0.00200000000000955s; LL=-3362.83441011363
TSP:unscaled:mds:2; time=0.00600000000000023s; LL=-3309.1531642465
R2E:unscaled:mds:2; time=0.00499999999999545s; LL=-3342.71043821784
HC:unscaled:mds:2; time=0.00199999999999534s; LL=-3486.62451825951
GW:unscaled:mds:2; time=0.00199999999999534s; LL=-3344.55965382229
OLO:unscaled:mds:2; time=0.00300000000000011s; LL=-3335.58320239201
TSP:scaled:pca:4; time=0.00499999999999545s; LL=-3298.95194684867
R2E:scaled:pca:4; time=0.00599999999998602s; LL=-3338.146149754
HC:scaled:pca:4; time=0.00199999999999534s; LL=-3442.74062925362
GW:scaled:pca:4; time=0.00300000000000011s; LL=-3339.8927441173
OLO:scaled:pca:4; time=0.00200000000000955s; LL=-3301.17616260978
TSP:unscaled:pca:4; time=0.00500000000000966s; LL=-3309.48135044702
R2E:unscaled:pca:4; time=0.00600000000000023s; LL=-3326.59663396091
HC:unscaled:pca:4; time=0.00300000000000011s; LL=-3504.74107976416
GW:unscaled:pca:4; time=0.00300000000000011s; LL=-3309.36747840491
OLO:unscaled:pca:4; time=0.00199999999999534s; LL=-3316.87195789112
TSP:scaled:kfa:4; time=0.0139999999999958s; LL=-3446.9702397748
R2E:scaled:kfa:4; time=0.0159999999999911s; LL=-3435.2639048946
HC:scaled:kfa:4; time=0.00199999999999534s; LL=-3474.58235010173
GW:scaled:kfa:4; time=0.00300000000000011s; LL=-3454.60105948887
OLO:scaled:kfa:4; time=0.00300000000000011s; LL=-3499.79026706372
TSP:unscaled:kfa:4; time=0.0139999999999958s; LL=-3375.3867058695
R2E:unscaled:kfa:4; time=0.0139999999999958s; LL=-3449.31629347224
HC:unscaled:kfa:4; time=0.00200000000000955s; LL=-3368.21944252585
GW:unscaled:kfa:4; time=0.00300000000000011s; LL=-3355.38217003777
OLO:unscaled:kfa:4; time=0.00300000000000011s; LL=-3393.58394308912
TSP:scaled:ica:4; time=0.012999999999991s; LL=-3469.37146386966
R2E:scaled:ica:4; time=0.0130000000000052s; LL=-3448.22987745296
HC:scaled:ica:4; time=0.00199999999999534s; LL=-3566.83088178542
GW:scaled:ica:4; time=0.00300000000000011s; LL=-3483.62224401728
OLO:scaled:ica:4; time=0.00300000000000011s; LL=-3398.95365331722
TSP:unscaled:ica:4; time=0.00799999999999557s; LL=-3343.45186788712
R2E:unscaled:ica:4; time=0.0310000000000059s; LL=-3482.51365151884
HC:unscaled:ica:4; time=0.00199999999999534s; LL=-3493.39402942921
GW:unscaled:ica:4; time=0.00300000000000011s; LL=-3419.92338477358
OLO:unscaled:ica:4; time=0.00300000000000011s; LL=-3413.41312164608
TSP:scaled:mds:4; time=0.00499999999999545s; LL=-3301.51913499388
R2E:scaled:mds:4; time=0.00600000000000023s; LL=-3338.146149754
HC:scaled:mds:4; time=0.00300000000000011s; LL=-3442.74062925362
GW:scaled:mds:4; time=0.00300000000000011s; LL=-3339.8927441173
OLO:scaled:mds:4; time=0.00199999999999534s; LL=-3301.17616260978
TSP:unscaled:mds:4; time=0.00499999999999545s; LL=-3329.74984682278
R2E:unscaled:mds:4; time=0.00600000000000023s; LL=-3326.59663396091
HC:unscaled:mds:4; time=0.00200000000000955s; LL=-3504.74107976416
GW:unscaled:mds:4; time=0.00300000000000011s; LL=-3309.36747840491
OLO:unscaled:mds:4; time=0.00300000000000011s; LL=-3316.87195789112
TSP:scaled:pca:8; time=0.00600000000000023s; LL=-3314.15469558275
R2E:scaled:pca:8; time=0.00600000000000023s; LL=-3327.08704247268
HC:scaled:pca:8; time=0.00199999999999534s; LL=-3491.02211775467
GW:scaled:pca:8; time=0.00300000000000011s; LL=-3304.58905466539
OLO:scaled:pca:8; time=0.00300000000000011s; LL=-3313.95497334427
TSP:unscaled:pca:8; time=0.00500000000000966s; LL=-3324.92914606585
R2E:unscaled:pca:8; time=0.00600000000000023s; LL=-3326.1743136559
HC:unscaled:pca:8; time=0.00300000000000011s; LL=-3336.87516701295
GW:unscaled:pca:8; time=0.00300000000000011s; LL=-3338.7600145505
OLO:unscaled:pca:8; time=0.00300000000000011s; LL=-3304.94036787816
TSP:scaled:kfa:8; time=0.0189999999999912s; LL=-3367.22098549417
R2E:scaled:kfa:8; time=0.019999999999996s; LL=-3415.05192110592
HC:scaled:kfa:8; time=0.00199999999999534s; LL=-3495.5319297394
GW:scaled:kfa:8; time=0.00400000000000489s; LL=-3304.55940833509
OLO:scaled:kfa:8; time=0.00199999999999534s; LL=-3345.38523988533
TSP:unscaled:kfa:8; time=0.0190000000000055s; LL=-3360.03671244763
R2E:unscaled:kfa:8; time=0.0189999999999912s; LL=-3375.46159137981
HC:unscaled:kfa:8; time=0.00300000000000011s; LL=-3440.07869282776
GW:unscaled:kfa:8; time=0.00300000000000011s; LL=-3349.57670608448
OLO:unscaled:kfa:8; time=0.00300000000000011s; LL=-3342.31645492951
TSP:scaled:ica:8; time=0.0559999999999974s; LL=-3377.45338345699
R2E:scaled:ica:8; time=0.0640000000000072s; LL=-3507.66955071625
HC:scaled:ica:8; time=0.00199999999999534s; LL=-3458.59081464692
GW:scaled:ica:8; time=0.00300000000000011s; LL=-3500.42327638865
OLO:scaled:ica:8; time=0.00300000000000011s; LL=-3444.53568524246
R2E:unscaled:ica:8; time=0.0169999999999959s; LL=-3558.88357437459
TSP:unscaled:ica:8; time=0.0580000000000069s; LL=-3415.52823660425
GW:unscaled:ica:8; time=0.00300000000000011s; LL=-3487.45666780099
HC:unscaled:ica:8; time=0.00199999999999534s; LL=-3585.25672443007
OLO:unscaled:ica:8; time=0.00200000000000955s; LL=-3439.81921135428
TSP:scaled:mds:8; time=0.00600000000000023s; LL=-3316.01759277146
HC:scaled:mds:8; time=0.00300000000000011s; LL=-3491.02211775467
R2E:scaled:mds:8; time=0.00600000000000023s; LL=-3327.08704247268
OLO:scaled:mds:8; time=0.00199999999999534s; LL=-3313.95497334427
GW:scaled:mds:8; time=0.00200000000000955s; LL=-3304.58905466539
TSP:unscaled:mds:8; time=0.00499999999999545s; LL=-3296.58664016952
R2E:unscaled:mds:8; time=0.00600000000000023s; LL=-3326.1743136559
HC:unscaled:mds:8; time=0.00200000000000955s; LL=-3336.87516701295
GW:unscaled:mds:8; time=0.00300000000000011s; LL=-3338.7600145505
OLO:unscaled:mds:8; time=0.00200000000000955s; LL=-3304.94036787816
Using ordering TSP:unscaled:none:1; LL=-3291.46182858414
Using ordering TSP:unscaled:mds:8; LL=-3296.58664016952
Joining, by = "c"
In file included from file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:1:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Core:531:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:2:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/LU:47:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Cholesky:12:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Jacobi:29:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Cholesky:43:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:4:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/QR:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Householder:27:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:5:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/SVD:48:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:6:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Geometry:58:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Dense:7:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Eigenvalues:58:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Sparse:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/SparseCore:66:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Sparse:27:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/OrderingMethods:71:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Sparse:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/SparseCholesky:43:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Sparse:32:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/SparseQR:35:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:31:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/Sparse:33:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:32:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/Eigen/CholmodSupport:45:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:35:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:39:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.cpp:3:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigen.h:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/RcppEigenForward.h:40:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/heterogeneous_system.hpp:34:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/dimension.hpp:21:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/heterogeneous_system.hpp:35:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/dimension.hpp:21:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/dimension_list.hpp:131:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/heterogeneous_system.hpp:39:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/linear_algebra.hpp:20:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:20:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/heterogeneous_system.hpp:40:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/unscale.hpp:28:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:20:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:29:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/conversion.hpp:17:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/detail/conversion_impl.hpp:21:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint.hpp:25:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26:
In file included from /tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token]
#include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
         ^
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/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 file1a6049709c8.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/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/random/negative_binomial_distribution.hpp:21:
/tmp/Rtmp9OOuy2/RLIBS_7e07d9a2612/BH/include/boost/random/poisson_distribution.hpp:338:9: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]
        struct {
        ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                              ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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;
                                                 ^
file1a6049709c8.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: file1a6049709c8.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