* installing *source* package ‘AlphaSimR’ ...
** this is package ‘AlphaSimR’ version ‘2.0.0’
** package ‘AlphaSimR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c MME.cpp -o MME.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c algorithm.cpp -o algorithm.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c alphaSuite.cpp -o alphaSuite.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c altAddTraitAD.cpp -o altAddTraitAD.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c calcGenParam.cpp -o calcGenParam.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c datastructures.cpp -o datastructures.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c getGeno.cpp -o getGeno.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c getGv.cpp -o getGv.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c getHybridGv.cpp -o getHybridGv.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ibd.cpp -o ibd.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c meiosis.cpp -o meiosis.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c misc.cpp -o misc.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c optimize.cpp -o optimize.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c packHaplo.cpp -o packHaplo.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c simulator.cpp -o simulator.o
In file included from MME.cpp:3:
In file included from ./alphasimr.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with ArmadiIn file included from lalphaSuite.cppl:o1 In file included from :
1RcppExports.cppIn file included from 4:./alphasimr.h.4:6:
4.In file included from :
3/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.hIn file included from .:/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h 29:P:
29/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.hl:
:e/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h71a::s7117e:: 17 c:warning: o Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]nwarning:
sUsing fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]i
der defining -DARMA _ 71U71 | S | E _ C U R R E N #T#p.pr raSagegmema a G mimetesHssusabag geie(s("s"UuUsesi in#ng4g 7 f5fa alfllolbrba acmckok r ceco.om"mp)pi
il la| at ^ti
ioonn wwiitthh AArrmmaaddiilllloo 1144..66..33.. PPlleeaassee ccoonnssiiddeerr ddeefining -DARMA_USE_fCiUnRiRnEgN T-.D ASReMeA _GUiStEH_uCbU RiRsEsNuTe. #S4e7e5 GfiotrH umbo ries.s"u)e
#| 4 ^7
5 for more.")
| ^
In file included from calcGenParam.cpp:1:
In file included from In file included from ./alphasimr.haltAddTraitAD.cpp::41:
:
In file included from In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h./alphasimr.h::294:
:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.hIn file included from :/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h71::2917:
:/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h :warning: 71Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]:
17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | 71 | # p r a g#mpar amgemsas amgees(s"aUgsei(n"gU sfianlgl bfaaclkl bcaocmkp icloamtpiiolna twiiotnh wAirtmha dAirlmlaod i1l4l.o6 .134.. 6P.l3e.a sPel ecaosnes icdoenrs iddeefri ndienfgi n-iDnAgR M-AD_AURSMEA__CUUSRER_ECNUTR.R ESNeTe. GSieteH uGbi tiHsusbu ei s#s4u7e5 #f4o7r5 mfoorre .m"o)r
e .| " ^)
| ^
In file included from getGeno.cpp:1:
In file included from ./alphasimr.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
In file included from getGv.cpp:1:
In file included from ./alphasimr.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.hIn file included from :getHybridGv.cpp71::117:
:In file included from ./alphasimr.hwarning: :Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]4
:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #prag m71a | m e s s a g e (#"pUrsaignmga fmaelslsbaagcek( "cUosmipnigl aftailolnb awcikt hc oAmrpmialdaitliloon 1w4i.t6h. 3A.r mPaldeialsleo c1o4n.s6i.d3e.r Pdleefaisnei ncgo n-sDiAdReMrA _dUeSfEi_nCiUnRgR E-NDTA.R MSAe_eU SGEi_tCHUuRbR EiNsTs.u eS e#e4 7G5i tfHourb miosrseu.e" )#
4 7| 5 ^
for more.")
| ^
In file included from misc.cpp:2:
In file included from ./alphasimr.h:4:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:In file included from 29meiosis.cpp:
:/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h1::
71In file included from :./alphasimr.h17::4 :
warning: In file included from Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h
:29:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
In file included from ibd.cpp71: | 1 :
In file included from ./alphasimr.h :71 4 | :
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h #: p29 r:
a/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h g: m71#a:p 17rm:ae gswarning: msUsing fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]aa
gmee(s"sUasgien(g" Ufsai ln71lg | b af ca kl l cb oa mc pk#i plcraoatmgipmoain l mawetisitsohan g Aewr(im"taUhds iiAlnrlgmo a fd1ai4ll.ll6ob. a31c.4k . PIn file included from 6clpackHaplo.cpp.oe:3ma1.ps:
ieIn file included from Pl ./alphasimr.hlac:eto4ain:
sosIn file included from eni/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h d:cwe29oir:
nt /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.hshd:i e71dAf:eri17rmn: ai ddnwarning: eigUsing fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]fl
il-noDi An1Rg4M .A-6_ D.U71A3S | R.E M _ APC _lU UeR RSa EEs N_e TC #.Ucp RorSaRnegEsemNi aTdG .eim rteS Hseduseeba f gGiieins(tis"HnuUugesb i -#niD4gsA7 sR5fuM aeAfl _ol#Urb4S a7Emc5_ok Cr fUecoR.orR"m E)pmN
ioT lr.| ae ^t.S
i"eo)en
Gw| ii ^tt
Hhu bA rimsasduiel l#o4 7154 .f6o.r3 .m oPrlee.a"s)e
c| o ^n
sider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
In file included from simulator.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more. [-W#pragma-messages]
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o AlphaSimR.so MME.o RcppExports.o algorithm.o alphaSuite.o altAddTraitAD.o calcGenParam.o datastructures.o getGeno.o getGv.o getHybridGv.o ibd.o meiosis.o misc.o optimize.o packHaplo.o simulator.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/AlphaSimR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/AlphaSimR.Rcheck/00LOCK-AlphaSimR/00new/AlphaSimR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AlphaSimR)