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amcdavid / HurdleNormal

Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression
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Installing HurdleNormal #4

Closed galaxywall closed 4 years ago

galaxywall commented 4 years ago

I was trying to install HurdleNormal from GitHub using the following command: devtools::install_github("amcdavid/HurdleNormal",dependencies = T) and got the following error message. Could you please help me figure out what is wrong?

Skipping 3 packages not available: MAST, Mus.musculus, netbenchmark Installing 20 packages: gridExtra, xfun, checkmate, jpeg, png, viridis, htmlTable, acepack, latticeExtra, Formula, RcppEigen, quadprog, Cairo, dtplyr, GGally, Hmisc, MAST, Mus.musculus, huge, directlabels Installing packages into ‘C:/Users/galaxywall/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) Error: Failed to install 'HurdleNormal' from GitHub: (converted from warning) packages ‘MAST’, ‘Mus.musculus’ are not available (for R version 3.6.2)

Also, to later intsall netbenchmark, Mus.musculus from Bioconductor, should I simply use a command like: BiocManager::install('netbenchmark')?

amcdavid commented 4 years ago

Yes, that's correct. Those packages are on bioconductor and will need to be installed as you indicated. I will update the Readme to make the clear. Thanks for the report.

On Fri, Jul 24, 2020, 7:43 PM galaxywall notifications@github.com wrote:

I was trying to install HurdleNormal from GitHub using the following command: devtools::install_github("amcdavid/HurdleNormal",dependencies = T) and got the following error message. Could you please help me figure out what is wrong?

Skipping 3 packages not available: MAST, Mus.musculus, netbenchmark Installing 20 packages: gridExtra, xfun, checkmate, jpeg, png, viridis, htmlTable, acepack, latticeExtra, Formula, RcppEigen, quadprog, Cairo, dtplyr, GGally, Hmisc, MAST, Mus.musculus, huge, directlabels Installing packages into ‘C:/Users/galaxywall/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) Error: Failed to install 'HurdleNormal' from GitHub: (converted from warning) packages ‘MAST’, ‘Mus.musculus’ are not available (for R version 3.6.2)

Also, to later intsall netbenchmark, Mus.musculus from Bioconductor, should I simply use a command like: BiocManager::install('netbenchmark')?

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galaxywall commented 4 years ago

Thanks. Do you have an idea why I got the error message when installing HurdleNormal from GitHub?

amcdavid commented 4 years ago

Looks like devtools doesn't know about bioconductor repositories. BiocManager::install('amcdavid/HurdleNormal') should install from github and knows about both cran and bioconductor.

FWIW, I don't think you have to set dependencies = TRUE unless you want to reproduce code from the paper or run some components of the vignette.

galaxywall commented 4 years ago

Eh, I tried your command and ended up with the following error. And I got the same error as I used my original command without setting dependencies = T.

BiocManager::install("amcdavid/HurdleNormal") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12) Installing github package(s) 'amcdavid/HurdleNormal' Downloading GitHub repo amcdavid/HurdleNormal@HEAD √ checking for file 'C:\Users\galaxywall\AppData\Local\Temp\RtmpWIcfig\remotes2f4c4e613893\amcdavid-HurdleNormal-f91e584/DESCRIPTION' (593ms)

  • preparing 'HurdleNormal': √ checking DESCRIPTION meta-information ...
  • cleaning src
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories Removed empty directory 'HurdleNormal/inst/aoas_simulations' Removed empty directory 'HurdleNormal/inst'
  • looking to see if a 'data/datalist' file should be added
  • building 'HurdleNormal_0.98.7.tar.gz'

*** arch - i386 C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"C:/Users/galaxywall/Documents/R/win-library/3.6/RcppArmadillo/include" -I"C:/Users/galaxywall/Documents/R/win-library/3.6/Rcpp/include" -O2 -Wall -mtune=generic -c hurdle_distributions.cpp -o hurdle_distributions.o C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"C:/Users/galaxywall/Documents/R/win-library/3.6/RcppArmadillo/include" -I"C:/Users/galaxywall/Documents/R/win-library/3.6/Rcpp/include" -O2 -Wall -mtune=generic -c hurdle_likelihood.cpp -o hurdle_likelihood.o C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o HurdleNormal.dll tmp.def hurdle_distributions.o hurdle_likelihood.o -LC:/PROGRA~1/R/R-36~1.2/bin/i386 -lR hurdle_likelihood.o:hurdlelikelihood.cpp:(.text+0x3e02): undefined reference to `dgemv' hurdle_likelihood.o:hurdlelikelihood.cpp:(.text+0x3ef2): undefined reference to `dgemv' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE]+0x12d): undefined reference to `dgemv' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE]+0x2d7): undefined reference to `dgemv' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE]+0x5b8): undefined reference to `dgemv' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma4gemvILb1ELb0ELb0EE15apply_blas_typeIdNS_3MatIdEEEEvPT_RKT0_PKS5_S5S5[ZN4arma4gemvILb1ELb0ELb0EE15apply_blas_typeIdNS_3MatIdEEEEvPT_RKT0_PKS5_S5S5]+0xc6): more undefined references to `dgemv_' follow hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4S4[ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4S4]+0x17a): undefined reference to dgemm_' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x397): undefined reference todsyrk_' collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'HurdleNormal'

amcdavid commented 4 years ago

Looks like there is some issue with your development stack. Can you compile other packages that use RcppArmadillo? Does install.packages('activegp', type='source') work, for example?

On Fri, Jul 24, 2020, 11:43 PM galaxywall notifications@github.com wrote:

Eh, I tried your command and ended up with the following error:

BiocManager::install("amcdavid/HurdleNormal") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12) Installing github package(s) 'amcdavid/HurdleNormal' Downloading GitHub repo amcdavid/HurdleNormal@HEAD √ checking for file 'C:\Users\galaxywall\AppData\Local\Temp\RtmpWIcfig\remotes2f4c4e613893\amcdavid-HurdleNormal-f91e584/DESCRIPTION' (593ms)

  • preparing 'HurdleNormal': √ checking DESCRIPTION meta-information ...

  • cleaning src

  • checking for LF line-endings in source and make files and shell scripts

  • checking for empty or unneeded directories Removed empty directory 'HurdleNormal/inst/aoas_simulations' Removed empty directory 'HurdleNormal/inst'

  • looking to see if a 'data/datalist' file should be added

  • building 'HurdleNormal_0.98.7.tar.gz'

  • installing source package 'HurdleNormal' ... using staged installation libs

*** arch - i386 C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/galaxywall/Documents/R/win-library/3.6/RcppArmadillo/include" -I"C:/Users/galaxywall/Documents/R/win-library/3.6/Rcpp/include" -O2 -Wall -mtune=generic -c hurdle_distributions.cpp -o hurdle_distributions.o C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/galaxywall/Documents/R/win-library/3.6/RcppArmadillo/include" -I"C:/Users/galaxywall/Documents/R/win-library/3.6/Rcpp/include" -O2 -Wall -mtune=generic -c hurdle_likelihood.cpp -o hurdle_likelihood.o C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o HurdleNormal.dll tmp.def hurdle_distributions.o hurdle_likelihood.o -LC:/PROGRA1/R/R-361.2/bin/i386 -lR hurdle_likelihood.o:hurdlelikelihood.cpp:(.text+0x3e02): undefined reference to dgemv' hurdle_likelihood.o:hurdlelikelihood.cpp:(.text+0x3ef2): undefined reference to dgemv'

hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE[ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE]+0x12d): undefined reference to dgemv' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10glue_timesEEE]+0x2d7): undefined reference to dgemv'

hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE[ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_3ColIdEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS7_T0_NS_10gluetimesEEE]+0x5b8): undefined reference to dgemv' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma4gemvILb1ELb0ELb0EE15apply_blas_typeIdNS_3MatIdEEEEvPT_RKT0_PKS5_S5S5[__ZN4arma4gemvILb1ELb0ELb0EE15apply_blas_typeIdNS_3MatIdEEEEvPT_RKT0_PKS5_S5S5]+0xc6): more undefined references to dgemv' follow hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$ ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4 [ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4S4]+0x17a): undefined reference to dgemm' hurdle_likelihood.o:hurdle_likelihood.cpp:(.text$_ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4S4[__ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4S4]+0x397): undefined reference to dsyrk' collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'HurdleNormal'

  • removing 'C:/Users/galaxywall/Documents/R/win-library/3.6/HurdleNormal' Error: Failed to install 'HurdleNormal' from GitHub: (converted from warning) installation of package ‘C:/Users/GALAXY~1/AppData/Local/Temp/RtmpWIcfig/file2f4c23a079ab/HurdleNormal_0.98.7.tar.gz’ had non-zero exit status

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galaxywall commented 4 years ago

It did work... I got the message "The downloaded source packages are in XXX".

amcdavid commented 4 years ago

Did you see evidence that they compiled and installed OK (eg, output from g++?) I don't have access to a windows machine currently, but some of your output makes my suspicious that you have mixed versions of Rtools (3.5) and R 3.6.

I can confirm that I can compile and install HurdleNormal fine on Mac and Linux.

galaxywall commented 4 years ago

I have attached the output below. Note that I tried uninstalled every R stuff in my laptop (there were indeed mixed versions of Rtools) and then reinstalled everything, but I kept getting the "non-zero exit status" error when trying installing HurdleNormal.

install.packages('activegp',type='source') Installing package into ‘C:/Users/galaxywall/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/activegp_1.0.4.tar.gz' Content type 'application/x-gzip' length 36632 bytes (35 KB) downloaded 35 KB

*** arch - i386 "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c C_GPcpp.cpp -o C_GPcpp.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hetGP_funcs.cpp -o hetGP_funcs.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernelexps.cpp -o kernelexps.o C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o activegp.dll tmp.def C_GPcpp.o RcppExports.o hetGP_funcs.o kernelexps.o -LC:/PROGRA~1/R/R-40~1.2/bin/i386 -lRlapack -LC:/PROGRA~1/R/R-40~1.2/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/PROGRA~1/R/R-40~1.2/bin/i386 -lR installing to C:/Users/galaxywall/Documents/R/win-library/4.0/00LOCK-activegp/00new/activegp/libs/i386

* arch - x64 "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c C_GPcpp.cpp -o C_GPcpp.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hetGP_funcs.cpp -o hetGP_funcs.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernelexps.cpp -o kernelexps.o C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o activegp.dll tmp.def C_GPcpp.o RcppExports.o hetGP_funcs.o kernelexps.o -LC:/PROGRA~1/R/R-40~1.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-40~1.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/PROGRA~1/R/R-40~1.2/bin/x64 -lR installing to C:/Users/galaxywall/Documents/R/win-library/4.0/00LOCK-activegp/00new/activegp/libs/x64 R byte-compile and prepare package for lazy loading * help installing help indices converting help for package 'activegp' finding HTML links ... done C_GP html
C_GP_ci html
C_GP_cpp html
C_Q html
C_tr html
C_var html
C_var2 html
W_kappa_ij html
W_kappa_ij2 html
W_kappa_ij_up html
activegp html
d1 html
domain_to_R html
domain_to_unit html
get_betagamma html
grad_W_kappa_ij2 html
grad_W_kappa_ij2_w2 html
grad_est_subspace html
logLikHessian html
n11_2_01 html
print.const_C html
subspace_dist html
update.const_C html
update_C2 html
building package indices testing if installed package can be loaded from temporary location arch - i386 arch - x64 testing if installed package can be loaded from final location ** arch - i386 arch - x64 ** testing if installed package keeps a record of temporary installation path

The downloaded source packages are in ‘C:\Users\galaxywall\AppData\Local\Temp\RtmpqW8S3V\downloaded_packages’

amcdavid commented 4 years ago

Ok, that looks like reasonable output from activegp, so I think we can rule out toolchain issues now.

What error message do that you get now from compiling HurdleNormal with the R4.0 stack? "non-zero exit status" isn't specific enough for me to help -- as I've said, HurdleNormal compiles fine on the systems I have access to. I don't have ready access to a windows machine so I am relying on your report to understand what might be going on.

On Jul 29, 2020, at 5:57 PM, galaxywall notifications@github.com wrote:

I have attached the output below. Note that I tried uninstalled every R stuff in my laptop (there were indeed mixed versions of Rtools) and then reinstalled everything, but I kept getting the "non-zero exit status" error when trying installing HurdleNormal.

install.packages('activegp',type='source') Installing package into ‘C:/Users/galaxywall/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/activegp_1.0.4.tar.gz https://cran.rstudio.com/src/contrib/activegp_1.0.4.tar.gz' Content type 'application/x-gzip' length 36632 bytes (35 KB) downloaded 35 KB

installing source package 'activegp' ... package 'activegp' successfully unpacked and MD5 sums checked using staged installation ** libs *** arch - i386 "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c C_GPcpp.cpp -o C_GPcpp.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hetGP_funcs.cpp -o hetGP_funcs.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernelexps.cpp -o kernelexps.o C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o activegp.dll tmp.def C_GPcpp.o RcppExports.o hetGP_funcs.o kernelexps.o -LC:/PROGRA1/R/R-401.2/bin/i386 -lRlapack -LC:/PROGRA1/R/R-401.2/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/PROGRA1/R/R-401.2/bin/i386 -lR installing to C:/Users/galaxywall/Documents/R/win-library/4.0/00LOCK-activegp/00new/activegp/libs/i386

* arch - x64 "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c C_GPcpp.cpp -o C_GPcpp.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hetGP_funcs.cpp -o hetGP_funcs.o "C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.2/include" -DNDEBUG -I'C:/Users/galaxywall/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/galaxywall/Documents/R/win-library/4.0/RcppArmadillo/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernelexps.cpp -o kernelexps.o C:/Users/galaxywall/Documents/R/win-library/4.0/lib/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o activegp.dll tmp.def C_GPcpp.o RcppExports.o hetGP_funcs.o kernelexps.o -LC:/PROGRA1/R/R-401.2/bin/x64 -lRlapack -LC:/PROGRA1/R/R-401.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/PROGRA1/R/R-401.2/bin/x64 -lR installing to C:/Users/galaxywall/Documents/R/win-library/4.0/00LOCK-activegp/00new/activegp/libs/x64 R byte-compile and prepare package for lazy loading * help installing help indices converting help for package 'activegp' finding HTML links ... done C_GP html C_GP_ci html C_GP_cpp html C_Q html C_tr html C_var html C_var2 html W_kappa_ij html W_kappa_ij2 html W_kappa_ij_up html activegp html d1 html domain_to_R html domain_to_unit html get_betagamma html grad_W_kappa_ij2 html grad_W_kappa_ij2_w2 html grad_est_subspace html logLikHessian html n11_2_01 html print.const_C html subspace_dist html update.const_C html update_C2 html building package indices testing if installed package can be loaded from temporary location arch - i386 arch - x64 testing if installed package can be loaded from final location ** arch - i386 arch - x64 ** testing if installed package keeps a record of temporary installation path

DONE (activegp) The downloaded source packages are in ‘C:\Users\galaxywall\AppData\Local\Temp\RtmpqW8S3V\downloaded_packages’

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galaxywall commented 4 years ago

I just installed Ubuntu in my computer and was able to move on to the body of your simulation codes. By the way, could you please tell me where I can find your data for T follicular helper cells? I can only locate your Shalek data from GitHub.

According to the corresponding paper, you used Gaussian based on the rough observation that the empirical distribution of log-transformed values is generally symmetric. Did you just observe that by making a density plot for each column?

amcdavid commented 4 years ago

Regarding normality, I think at some point we did some goodness of fit testing in the preparation of writing Finak et al 2015 though nothing that made it into the paper. This was a while ago and I'm a bit fuzzy on the details, so make what of that you will. With sufficient same size, I would be astonished if you could accept normality marginally. And of course, being marginally normal certainly doesn't mean that the distribution is conditionally normal (unless besides the margins, each and every other linear combination is normal...)

Let me know what your email is, and I will send you the T follicular helper cells. I am not able to post them publicly but happy to share upon request.

galaxywall commented 4 years ago

My email address is: harvey961001@gmail.com. Thanks.

galaxywall commented 4 years ago

I just got the error message "object 'contaminate' not found" when running the for loop containing "contam = switch(modelArgs[i,'contam'], t=contaminate, none=NA, selection=selectionModel)" in your "simulations.R" file. Do you have an idea what that error is about? Is it related to the source() and install() from the previous lines?

amcdavid commented 4 years ago

You probably need to source('simulation-library.R'): https://github.com/amcdavid/HurdleNormal/search?q=contaminate&unscoped_q=contaminate