glmGamPoi 1.0.0
Constantin Ahlmann-Eltze
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/glmGamPoi |
| Branch: RELEASE_3_11 |
| Last Commit: ea2224c |
| Last Changed Date: 2020-04-27 15:35:32 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/glmGamPoi_1.0.0.tar.gz && rm -rf glmGamPoi.buildbin-libdir && mkdir glmGamPoi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=glmGamPoi.buildbin-libdir glmGamPoi_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL glmGamPoi_1.0.0.zip && rm glmGamPoi_1.0.0.tar.gz glmGamPoi_1.0.0.zip
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install for i386
* installing *source* package 'glmGamPoi' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c beta_estimation.cpp -o beta_estimation.o
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:74:72: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:77:75: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
beta_estimation.cpp: In instantiation of 'void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]':
beta_estimation.cpp:27:36: required from here
beta_estimation.cpp:15:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < v.n_elem; i++){
~~^~~~~~~~~~
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = int]':
beta_estimation.cpp:121:45: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, double, double, int, bool) [with NumericType = int; BMNumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:169:101: required from here
../inst/include/deviance.h:51:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for (int i = 0; i < Y.n_elem; i++) {
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = double]':
beta_estimation.cpp:121:45: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, double, double, int, bool) [with NumericType = double; BMNumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:175:104: required from here
../inst/include/deviance.h:51:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c deviance.cpp -o deviance.o
In file included from deviance.cpp:3:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:74:72: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:77:75: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c overdispersion.cpp -o overdispersion.o
overdispersion.cpp: In instantiation of 'Rcpp::NumericVector estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double) [with NumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:237:143: required from here
overdispersion.cpp:209:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:209:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp: In instantiation of 'Rcpp::NumericVector estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double) [with NumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:239:143: required from here
overdispersion.cpp:209:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:209:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o glmGamPoi.dll tmp.def RcppExports.o beta_estimation.o deviance.o overdispersion.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/glmGamPoi.buildbin-libdir/00LOCK-glmGamPoi/00new/glmGamPoi/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'glmGamPoi'
finding HTML links ... done
as.list.glmGamPoi html
estimate_betas_fisher_scoring html
estimate_betas_one_group html
estimate_betas_roughly html
estimate_betas_roughly_one_group html
estimate_overdispersions html
estimate_size_factors html
format_matrix html
gampoi_overdispersion_mle html
glm_gp html
finding level-2 HTML links ... done
glm_gp_impl html
print.glmGamPoi html
residuals.glmGamPoi html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'glmGamPoi' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c beta_estimation.cpp -o beta_estimation.o
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:74:72: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:77:75: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
beta_estimation.cpp: In instantiation of 'void clamp_inplace(arma::Mat<eT>&, double, double) [with NumericType = double]':
beta_estimation.cpp:27:36: required from here
beta_estimation.cpp:15:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < v.n_elem; i++){
~~^~~~~~~~~~
In file included from beta_estimation.cpp:6:
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = int]':
beta_estimation.cpp:121:45: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, double, double, int, bool) [with NumericType = int; BMNumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:169:101: required from here
../inst/include/deviance.h:51:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for (int i = 0; i < Y.n_elem; i++) {
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'double compute_gp_deviance_sum(const arma::Mat<eT>&, const arma::Mat<double>&, double) [with NumericType = double]':
beta_estimation.cpp:121:45: required from 'Rcpp::List fitBeta_fisher_scoring_impl(Rcpp::RObject, const mat&, Rcpp::RObject, Rcpp::NumericVector, SEXP, double, double, int, bool) [with NumericType = double; BMNumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; arma::mat = arma::Mat<double>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; SEXP = SEXPREC*]'
beta_estimation.cpp:175:104: required from here
../inst/include/deviance.h:51:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c deviance.cpp -o deviance.o
In file included from deviance.cpp:3:
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = int; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:74:72: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for(int i = 0; i < Y.n_elem; i++){
~~^~~~~~~~~~
../inst/include/deviance.h: In instantiation of 'arma::Mat<double> compute_gp_deviance_residuals_matrix_impl(arma::Mat<eT>, arma::Mat<double>, Rcpp::NumericVector) [with NumericType = double; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
../inst/include/deviance.h:77:75: required from here
../inst/include/deviance.h:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c overdispersion.cpp -o overdispersion.o
overdispersion.cpp: In instantiation of 'Rcpp::NumericVector estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double) [with NumericType = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:237:143: required from here
overdispersion.cpp:209:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:209:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp: In instantiation of 'Rcpp::NumericVector estimate_overdispersions_fast_internal(Rcpp::RObject, Rcpp::RObject, Rcpp::NumericMatrix, bool, double) [with NumericType = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::NumericMatrix = Rcpp::Matrix<14>]':
overdispersion.cpp:239:143: required from here
overdispersion.cpp:209:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
overdispersion.cpp:209:54: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if(n_genes != mean_mat_bm->get_nrow() || n_samples != mean_mat_bm->get_ncol()){
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o glmGamPoi.dll tmp.def RcppExports.o beta_estimation.o deviance.o overdispersion.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/glmGamPoi.buildbin-libdir/glmGamPoi/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'glmGamPoi' as glmGamPoi_1.0.0.zip
* DONE (glmGamPoi)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'glmGamPoi' successfully unpacked and MD5 sums checked