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grattan / covid19.model.sa2

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Error in installing from master branch #55

Closed wfmackey closed 4 years ago

wfmackey commented 4 years ago

Missing a hutilscpp export and3s:

> remotes::install_github("hughparsonage/hutilscpp")
Skipping install of 'hutilscpp' from a github remote, the SHA1 (31b6d976) has not changed since last install.
  Use `force = TRUE` to force installation
> remotes::install_github("grattan/covid19.model.sa2")
Downloading GitHub repo grattan/covid19.model.sa2@master
Skipping 1 packages ahead of CRAN: data.table
✓  checking for file ‘/private/var/folders/g2/728t399s5gbbk6bgj5ndlgy1w8w938/T/Rtmp1nZMzE/remotes102912e5f0001/grattan-covid19.model.sa2-668b09481cb2849a5d42b3189db08c611302abe6/DESCRIPTION’ (583ms)
─  preparing ‘covid19.model.sa2’: (8.3s)
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts (2.2s)
─  checking for empty or unneeded directories
─  building ‘covid19.model.sa2_0.23.0.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/Users/mackeyw/Library/R/4.0/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘covid19.model.sa2’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c assertions.cpp -o assertions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c distr2status.cpp -o distr2status.o
distr2status.cpp:104:9: warning: unused variable 'local_today' [-Wunused-variable]
    int local_today = LocalContact[day] + LocalUnknown[day] + UnderInvestigation[day];
        ^
distr2status.cpp:90:7: warning: unused variable 'n_active' [-Wunused-variable]
  int n_active = CumCases[0];
      ^
distr2status.cpp:57:7: warning: unused variable 'final_yday' [-Wunused-variable]
  int final_yday = Healed[nh - 1];
      ^
distr2status.cpp:97:7: warning: unused variable 'i_Local' [-Wunused-variable]
  int i_Local = 0;
      ^
distr2status.cpp:91:7: warning: unused variable 'n_healed' [-Wunused-variable]
  int n_healed = Healed[0];
      ^
distr2status.cpp:92:7: warning: unused variable 'n_killed' [-Wunused-variable]
  int n_killed = Killed[0];
      ^
distr2status.cpp:56:7: warning: unused variable 'first_yday' [-Wunused-variable]
  int first_yday= Healed[0];
      ^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_aus_simulate.cpp -o do_aus_simulate.o
do_aus_simulate.cpp:1448:9: warning: unused variable 'statei' [-Wunused-variable]
    int statei = stateShortSA2[sa2i];
        ^
do_aus_simulate.cpp:1487:9: warning: unused variable 'd' [-Wunused-variable]
    int d = sa2_final - sa2_first;
        ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_exp_dbl2int.cpp -o do_exp_dbl2int.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_lag.cpp -o do_lag.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_seqN_N.cpp -o do_seqN_N.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_workplaces.cpp -o do_workplaces.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c openmp-test.cpp -o openmp-test.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c postcode_to_sa2_sorted.cpp -o postcode_to_sa2_sorted.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c random-variable-dqrng.cpp -o random-variable-dqrng.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c random-variables.cpp -o random-variables.o
random-variables.cpp:192:20: warning: unused function 'splitmix64_seed' [-Wunused-function]
static inline void splitmix64_seed(uint64_t seed) { splitmix64_x = seed; }
                   ^
random-variables.cpp:206:24: warning: unused function 'splitmix64_cast32' [-Wunused-function]
static inline uint32_t splitmix64_cast32(void) {
                       ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sa2-lats.cpp -o sa2-lats.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sa2-lons.cpp -o sa2-lons.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sa2_dist.cpp -o sa2_dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c short_sa2.cpp -o short_sa2.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/mackeyw/Library/R/4.0/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dqrng/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c which_unsorted.cpp -o which_unsorted.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o covid19.model.sa2.so RcppExports.o assertions.o distr2status.o do_aus_simulate.o do_exp_dbl2int.o do_lag.o do_seqN_N.o do_workplaces.o openmp-test.o postcode_to_sa2_sorted.o random-variable-dqrng.o random-variables.o sa2-lats.o sa2-lons.o sa2_dist.o short_sa2.o utils.o which_unsorted.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/mackeyw/Library/R/4.0/library/00LOCK-covid19.model.sa2/00new/covid19.model.sa2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘and3s’ is not exported by 'namespace:hutilscpp'
Execution halted
ERROR: lazy loading failed for package ‘covid19.model.sa2’
* removing ‘/Users/mackeyw/Library/R/4.0/library/covid19.model.sa2’
* restoring previous ‘/Users/mackeyw/Library/R/4.0/library/covid19.model.sa2’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/g2/728t399s5gbbk6bgj5ndlgy1w8w938/T//Rtmp1nZMzE/file102915ef9596f/covid19.model.sa2_0.23.0.tar.gz’ had non-zero exit status
wfmackey commented 4 years ago

Yep works for me now