I suddenly became unable to publish my app onto RStudio Connect, and I am not sure what the cause is. It is failing because of an error with lme4 and/or R snapshot restore. There app runs locally and I published it successfully a few days ago with no problems.
Here is the output from the log file:
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g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glmFamily.cpp -o glmFamily.o
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g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optimizer.cpp -o optimizer.o
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g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c predModule.cpp -o predModule.o
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g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c respModule.cpp -o respModule.o
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In file included from predModule.h:13:0,
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from predModule.cpp:8:
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lme4CholmodDecomposition.h:20:72: error: expected template-name before ‘<’ token
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class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
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^
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lme4CholmodDecomposition.h:20:72: error: expected ‘{’ before ‘<’ token
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In file included from predModule.h:13:0,
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from predModule.cpp:8:
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lme4CholmodDecomposition.h: In function ‘SEXPREC* lme4::Eigen_cholmod_wrap(const lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<Scalar> >&)’:
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lme4CholmodDecomposition.h:77:15: error: ‘cholmod_factor’ does not name a type; did you mean ‘chkder_factor’?
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const cholmod_factor* f = obj.factor();
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^~~~~~~~~~~~~~
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chkder_factor
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lme4CholmodDecomposition.h:78:13: error: ‘f’ was not declared in this scope
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if (f->minor < f->n)
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^
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lme4CholmodDecomposition.h:82:36: error: ‘f’ was not declared in this scope
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::Rcpp::S4 ans(std::string(f->is_super ? "dCHMsuper" : "dCHMsimpl"));
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^
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In file included from predModule.cpp:8:0:
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predModule.h: At global scope:
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predModule.h:40:23: error: field ‘d_L’ has incomplete type ‘lme4::merPredD::ChmDecomp {aka lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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ChmDecomp d_L;
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^~~
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In file included from predModule.h:13:0,
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from predModule.cpp:8:
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lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
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^~~~~~~~~~~~~~~~~~~~~~~~
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In file included from predModule.h:13:0,
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from external.cpp:8:
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lme4CholmodDecomposition.h:20:72: error: expected template-name before ‘<’ token
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class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
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^
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lme4CholmodDecomposition.h:20:72: error: expected ‘{’ before ‘<’ token
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In file included from predModule.h:13:0,
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from external.cpp:8:
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lme4CholmodDecomposition.h: In function ‘SEXPREC* lme4::Eigen_cholmod_wrap(const lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<Scalar> >&)’:
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lme4CholmodDecomposition.h:77:15: error: ‘cholmod_factor’ does not name a type; did you mean ‘chkder_factor’?
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const cholmod_factor* f = obj.factor();
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^~~~~~~~~~~~~~
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chkder_factor
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lme4CholmodDecomposition.h:78:13: error: ‘f’ was not declared in this scope
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if (f->minor < f->n)
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^
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lme4CholmodDecomposition.h:82:36: error: ‘f’ was not declared in this scope
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::Rcpp::S4 ans(std::string(f->is_super ? "dCHMsuper" : "dCHMsimpl"));
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^
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predModule.cpp: In member function ‘Rcpp::List lme4::merPredD::condVar(const Environment&) const’:
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predModule.cpp:122:43: error: ‘CHOLMOD_A’ was not declared in this scope
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d_L.solveInPlace(LvT, CHOLMOD_A);
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^~~~~~~~~
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In file included from external.cpp:8:0:
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predModule.h: At global scope:
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predModule.h:40:23: error: field ‘d_L’ has incomplete type ‘lme4::merPredD::ChmDecomp {aka lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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ChmDecomp d_L;
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^~~
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In file included from predModule.h:13:0,
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from external.cpp:8:
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lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
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^~~~~~~~~~~~~~~~~~~~~~~~
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external.cpp: In function ‘SEXPREC* glmerAGQ(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
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external.cpp:437:18: error: invalid use of incomplete type ‘const ChmDecomp {aka const class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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if (pp->L().factor()->nzmax != q)
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~~~~~^~
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In file included from predModule.h:13:0,
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from external.cpp:8:
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lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
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^~~~~~~~~~~~~~~~~~~~~~~~
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external.cpp:439:49: error: invalid use of incomplete type ‘const ChmDecomp {aka const class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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const Ar1 sd(MAr1((double*)pp->L().factor()->x, q).inverse());
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~~~~~^~
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In file included from predModule.h:13:0,
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from external.cpp:8:
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lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
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class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
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Unable to fully restore the R packages associated with this deployment.
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Please review the preceding messages to determine which package
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encountered installation difficulty and the cause of the failure.
Here is the output from the Deploy tab in Rstudio:
curl: HTTP 200 https://cran.rstudio.com/src/contrib/Archive/lme4/lme4_1.1-34.tar.gz
[1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/usr/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/Rtmpbc5bvi/packrat-install-6dfd3e5d03fb/lme4' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package ‘lme4’ ...\n** package ‘lme4’ successfully unpacked and MD5 sums checked\n** using staged installation\n** libs\nusing C++ compiler: ‘g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0’\ng++ -std=gnu++17 -I\"/usr/share/R/include\" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=
2 -c external.cpp -o external.o\ng++ -std=gnu++17 -I\"/usr/share/R/include\" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glmFamily.cpp -o glmFamily.o\ng++ -std=gnu++17 -I\"/usr/share/R/include\" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optimizer.cpp -o optimizer.o\ng++ -std=gnu++17 -I\"/usr/share/R/include\" -DNDEBUG -I'/opt/rstudio-connect/mn
t/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c predModule.cpp -o predModule.o\ng++ -std=gnu++17 -I\"/usr/share/R/include\" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c respModule.cpp -o respModule.o\nIn file included from predModule.h:13:0,\n from predModule.cpp:8:\nlme4CholmodDecomposition.h:20:72: error: expected template-name before ‘<’ token\n class lme4Cholmo
dDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {\n ^\nlme4CholmodDecomposition.h:20:72: error: expected ‘{’ before ‘<’ token\nIn file included from predModule.h:13:0,\n from predModule.cpp:8:\nlme4CholmodDecomposition.h: In function ‘SEXPREC* lme4::Eigen_cholmod_wrap(const lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<Scalar> >&)’:\nlme4CholmodDecomposition.h:77:15: error: ‘cholmod_factor’ does not name a type; did you mean ‘chkder_factor’?\n const cholmod_factor* f = obj.factor();\n ^~~~~~~~~~~~~~\n chkder_factor\nlme4CholmodDecomposition.h:78:13: error: ‘f’ was not declared in this scope\n if (f->minor < f->n)\n ^\nlme4CholmodDecomposition.h:82:36: error: ‘f’ was not declared in this scope\n ::Rcpp::S4 ans(std::string(f->is_super ? \"dCHMsuper\" : \"dCHMsimpl\"));\n ^
\nIn file included from predModule.cpp:8:0:\npredModule.h: At global scope:\npredModule.h:40:23: error: field ‘d_L’ has incomplete type ‘lme4::merPredD::ChmDecomp {aka lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n ChmDecomp d_L;\n ^~~\nIn file included from predModule.h:13:0,\n from predModule.cpp:8:\nlme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {\n ^~~~~~~~~~~~~~~~~~~~~~~~\nIn file included from predModule.h:13:0,\n from external.cpp:8:\nlme4CholmodDecomposition.h:20:72: error: expected template-name before ‘<’ token\n class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {\n
^\nlme4CholmodDecomposition.h:20:72: error: expected ‘{’ before ‘<’ token\nIn file included from predModule.h:13:0,\n from external.cpp:8:\nlme4CholmodDecomposition.h: In function ‘SEXPREC* lme4::Eigen_cholmod_wrap(const lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<Scalar> >&)’:\nlme4CholmodDecomposition.h:77:15: error: ‘cholmod_factor’ does not name a type; did you mean ‘chkder_factor’?\n const cholmod_factor* f = obj.factor();\n ^~~~~~~~~~~~~~\n chkder_factor\nlme4CholmodDecomposition.h:78:13: error: ‘f’ was not declared in this scope\n if (f->minor < f->n)\n ^\nlme4CholmodDecomposition.h:82:36: error: ‘f’ was not declared in this scope\n ::Rcpp::S4 ans(std::string(f->is_super ? \"dCHMsuper\" : \"dCHMsimpl\"));\n ^\npredModule.cpp: In member function ‘Rcpp::List lme4::merPredD::condVar(const Environment&) const’:\npredModule.cpp:122:43: error: ‘CHOLMOD_A
’ was not declared in this scope\n d_L.solveInPlace(LvT, CHOLMOD_A);\n ^~~~~~~~~\nIn file included from external.cpp:8:0:\npredModule.h: At global scope:\npredModule.h:40:23: error: field ‘d_L’ has incomplete type ‘lme4::merPredD::ChmDecomp {aka lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n ChmDecomp d_L;\n ^~~\nIn file included from predModule.h:13:0,\n from external.cpp:8:\nlme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {\n ^~~~~~~~~~~~~~~~~~~~~~~~\nexternal.cpp: In function ‘SEXPREC* glmerAGQ(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:\nexternal.cpp:437:18: error: invalid use of incomplete type ‘const ChmDecomp {aka const class lme4:
:lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n if (pp->L().factor()->nzmax != q)\n ~~~~~^~\nIn file included from predModule.h:13:0,\n from external.cpp:8:\nlme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {\n ^~~~~~~~~~~~~~~~~~~~~~~~\nexternal.cpp:439:49: error: invalid use of incomplete type ‘const ChmDecomp {aka const class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’\n const Ar1 sd(MAr1((double*)pp->L().factor()->x, q).inverse());\n ~~~~~^~\nIn file included from predModule.h:13:0,\n from external.cpp:8:\nlme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposi
tion<Eigen::SparseMatrix<double, 0, int> >}’\n class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {\n ^~~~~~~~~~~~~~~~~~~~~~~~\npredModule.cpp: In member function ‘void lme4::merPredD::updateL()’:\npredModule.cpp:154:20: error: ‘::M_chm_factor_ldetL2’ has not been declared\n d_ldL2 = ::M_chm_factor_ldetL2(d_L.factor());\n ^~~~~~~~~~~~~~~~~~~\npredModule.cpp: In member function ‘lme4::merPredD::Scalar lme4::merPredD::solve()’:\npredModule.cpp:186:34: error: ‘CHOLMOD_P’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_P);\n ^~~~~~~~~\npredModule.cpp:187:34: error: ‘CHOLMOD_L’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_L); // d_delu now contains cu\n ^~~~~~~~~\npredModule.cpp:195:34: error: ‘CHOLMOD_Lt’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_Lt);\n
^~~~~~~~~~\npredModule.cpp:195:34: note: suggested alternative: ‘COLAMD_OK’\n d_L.solveInPlace(d_delu, CHOLMOD_Lt);\n ^~~~~~~~~~\n COLAMD_OK\npredModule.cpp:196:34: error: ‘CHOLMOD_Pt’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_Pt);\n ^~~~~~~~~~\npredModule.cpp:196:34: note: suggested alternative: ‘COLAMD_OK’\n d_L.solveInPlace(d_delu, CHOLMOD_Pt);\n ^~~~~~~~~~\n COLAMD_OK\npredModule.cpp: In member function ‘lme4::merPredD::Scalar lme4::merPredD::solveU()’:\npredModule.cpp:203:34: error: ‘CHOLMOD_P’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_P);\n ^~~~~~~~~\npredModule.cpp:204:34: error: ‘CHOLMOD_L’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_L); // d_d
elu now contains cu\n ^~~~~~~~~\npredModule.cpp:206:34: error: ‘CHOLMOD_Lt’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_Lt);\n ^~~~~~~~~~\npredModule.cpp:206:34: note: suggested alternative: ‘COLAMD_OK’\n d_L.solveInPlace(d_delu, CHOLMOD_Lt);\n ^~~~~~~~~~\n COLAMD_OK\npredModule.cpp:207:34: error: ‘CHOLMOD_Pt’ was not declared in this scope\n d_L.solveInPlace(d_delu, CHOLMOD_Pt);\n ^~~~~~~~~~\npredModule.cpp:207:34: note: suggested alternative: ‘COLAMD_OK’\n d_L.solveInPlace(d_delu, CHOLMOD_Pt);\n ^~~~~~~~~~\n COLAMD_OK\npredModule.cpp: In member function ‘void lme4::merPredD::updateDecomp(const MatrixXd*)’:\npredModule.cpp:279:37: error: ‘CHOLMOD_P’ was not declared in this scope\n d_L.solveIn
Place(d_RZX, CHOLMOD_P);\n ^~~~~~~~~\npredModule.cpp:280:37: error: ‘CHOLMOD_L’ was not declared in this scope\n d_L.solveInPlace(d_RZX, CHOLMOD_L);\n ^~~~~~~~~\npredModule.cpp: In member function ‘void lme4::merPredD::MCMC_beta_u(const Scalar&)’:\npredModule.cpp:346:32: error: ‘CHOLMOD_Lt’ was not declared in this scope\n d_L.solveInPlace(del1, CHOLMOD_Lt);\n ^~~~~~~~~~\npredModule.cpp:346:32: note: suggested alternative: ‘COLAMD_OK’\n d_L.solveInPlace(del1, CHOLMOD_Lt);\n ^~~~~~~~~~\n COLAMD_OK\n/usr/lib/R/etc/Makeconf:200: recipe for target 'external.o' failed\nmake: *** [external.o] Error 1\nmake: *** Waiting for unfinished jobs....\n/usr/lib/R/etc/Makeconf:200: recipe for target 'predModule.o' failed\nmake: *** [predModule.o] Error 1\nERROR: compilation failed for package ‘lme4’\n* removing ‘/
opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/lme4’"
Error: Command failed (1)
Failed to run system command:
'/usr/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/Rtmpbc5bvi/packrat-install-6dfd3e5d03fb/lme4' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0' --install-tests --no-docs --no-multiarch --no-demo
The command failed with output:
* installing *source* package ‘lme4’ ...
** package ‘lme4’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c external.cpp -o external.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glmFamily.cpp -o glmFamily.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optimizer.cpp -o optimizer.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c predModule.cpp -o predModule.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/Rcpp/include' -I'/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.3.0/RcppEigen/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/build/r-base-cRDaP8/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c respModule.cpp -o respModule.o
In file included from predModule.h:13:0,
from predModule.cpp:8:
lme4CholmodDecomposition.h:20:72: error: expected template-name before ��<’ token
class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
^
lme4CholmodDecomposition.h:20:72: error: expected ‘{’ before ‘<’ token
In file included from predModule.h:13:0,
from predModule.cpp:8:
lme4CholmodDecomposition.h: In function ‘SEXPREC* lme4::Eigen_cholmod_wrap(const lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<Scalar> >&)’:
lme4CholmodDecomposition.h:77:15: error: ‘cholmod_factor’ does not name a type; did you mean ‘chkder_factor’?
const cholmod_factor* f = obj.factor();
^~~~~~~~~~~~~~
chkder_factor
lme4CholmodDecomposition.h:78:13: error: ‘f’ was not declared in this scope
if (f->minor < f->n)
^
lme4CholmodDecomposition.h:82:36: error: ‘f’ was not declared in this scope
::Rcpp::S4 ans(std::string(f->is_super ? "dCHMsuper" : "dCHMsimpl"));
^
In file included from predModule.cpp:8:0:
predModule.h: At global scope:
predModule.h:40:23: error: field ‘d_L’ has incomplete type ‘lme4::merPredD::ChmDecomp {aka lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
ChmDecomp d_L;
^~~
In file included from predModule.h:13:0,
from predModule.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
^~~~~~~~~~~~~~~~~~~~~~~~
In file included from predModule.h:13:0,
from external.cpp:8:
lme4CholmodDecomposition.h:20:72: error: expected template-name before ‘<’ token
class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
^
lme4CholmodDecomposition.h:20:72: error: expected ‘{’ before ‘<’ token
In file included from predModule.h:13:0,
from external.cpp:8:
lme4CholmodDecomposition.h: In function ‘SEXPREC* lme4::Eigen_cholmod_wrap(const lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<Scalar> >&)’:
lme4CholmodDecomposition.h:77:15: error: ‘cholmod_factor’ does not name a type; did you mean ‘chkder_factor’?
const cholmod_factor* f = obj.factor();
^~~~~~~~~~~~~~
chkder_factor
lme4CholmodDecomposition.h:78:13: error: ‘f’ was not declared in this scope
if (f->minor < f->n)
^
lme4CholmodDecomposition.h:82:36: error: ‘f’ was not declared in this scope
::Rcpp::S4 ans(std::string(f->is_super ? "dCHMsuper" : "dCHMsimpl"));
^
predModule.cpp: In member function ‘Rcpp::List lme4::merPredD::condVar(const Environment&) const’:
predModule.cpp:122:43: error: ‘CHOLMOD_A’ was not declared in this scope
d_L.solveInPlace(LvT, CHOLMOD_A);
^~~~~~~~~
In file included from external.cpp:8:0:
predModule.h: At global scope:
predModule.h:40:23: error: field ‘d_L’ has incomplete type ‘lme4::merPredD::ChmDecomp {aka lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
ChmDecomp d_L;
^~~
In file included from predModule.h:13:0,
from external.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
^~~~~~~~~~~~~~~~~~~~~~~~
external.cpp: In function ‘SEXPREC* glmerAGQ(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
external.cpp:437:18: error: invalid use of incomplete type ‘const ChmDecomp {aka const class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
if (pp->L().factor()->nzmax != q)
~~~~~^~
In file included from predModule.h:13:0,
from external.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
^~~~~~~~~~~~~~~~~~~~~~~~
external.cpp:439:49: error: invalid use of incomplete type ‘const ChmDecomp {aka const class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
const Ar1 sd(MAr1((double*)pp->L().factor()->x, q).inverse());
~~~~~^~
In file included from predModule.h:13:0,
from external.cpp:8:
lme4CholmodDecomposition.h:20:11: note: declaration of ‘lme4::merPredD::ChmDecomp {aka class lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >}’
class lme4CholmodDecomposition : public Eigen::CholmodDecomposition<_MatrixType, _UpLo> {
Unable to fully restore the R packages associated with this deployment.
Please review the preceding messages to determine which package
encountered installation difficulty and the cause of the failure.
Build error: exit status 1
── Deployment complete ─────────────────────────────────────────────────────────
✖ Deployment failed with error: exit status 1