Can't install glmGamPoi in almalinux system

[RenJ-Feng]

BiocManager::install("glmGamPoi")
return std::make_unique<DelayedBinaryIsometricOperation_internal::DenseSimpleBlock<oracle_, OutputValue_, InputValue_, Index_, Operation_> >(
~
my_left.get(),
~~~~~~~~~~~~~~
my_right.get(),
~~~~~~~~~~~~~~~
my_operation,
~~~~~~~~~~~~~
row,
~~~~
std::move(oracle),
~~~~~~~~~~~~~~~~~~
block_start,
~~~~~~~~~~~~
block_length,
~~~~~~~~~~~~^
opt
~~~
);
~
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp: In instantiation of ‘std::unique_ptr<typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type> tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense_expanded_internal(bool, tatami::MaybeOracle<oracle_, Index_>, tatami::VectorPtr<Index_>, const tatami::Options&) const [with bool oracle_ = true; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)0>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::OracularDenseExtractor<double, int>; tatami::MaybeOracle<oracle_, Index_> = std::shared_ptr<const tatami::Oracle >; tatami::VectorPtr<Index_> = std::shared_ptr<const std::vector >]’:
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:686:60: required from ‘std::unique_ptr<typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type> tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense_internal(bool, Args_&& ...) const [with bool oracle_ = true; Args_ = {std::shared_ptr<const tatami::Oracle >, std::shared_ptr<const std::vector<int, std::allocator > >, const tatami::Options&}; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)0>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::OracularDenseExtractor<double, int>]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:807:36: required from ‘std::unique_ptr<tatami::OracularDenseExtractor<OutputValue_, Index_> > tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense(bool, std::shared_ptr<const tatami::Oracle<Index_> >, tatami::VectorPtr<Index_>, const tatami::Options&) const [with OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)0>; tatami::VectorPtr<Index_> = std::shared_ptr<const std::vector >]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:806:68: required from here
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:673:13: 警告：right operand of comma operator has no effect [-Wunused-value]
my_operation,
^~~~~~~~~~~~
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:674:16: 警告：right operand of comma operator has no effect [-Wunused-value]
row,
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp: In instantiation of ‘std::unique_ptr<typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type> tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense_simple_internal(bool, tatami::MaybeOracle<oracle_, Index_>, tatami::VectorPtr<Index_>, const tatami::Options&) const [with bool oracle_ = true; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)0>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::OracularDenseExtractor<double, int>; tatami::MaybeOracle<oracle_, Index_> = std::shared_ptr<const tatami::Oracle >; tatami::VectorPtr<Index_> = std::shared_ptr<const std::vector >]’:
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:691:46: required from ‘std::unique_ptr<typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type> tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense_internal(bool, Args_&& ...) const [with bool oracle_ = true; Args_ = {std::shared_ptr<const tatami::Oracle >, std::shared_ptr<const std::vector<int, std::allocator > >, const tatami::Options&}; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)0>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::OracularDenseExtractor<double, int>]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:807:36: required from ‘std::unique_ptr<tatami::OracularDenseExtractor<OutputValue_, Index_> > tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense(bool, std::shared_ptr<const tatami::Oracle<Index_> >, tatami::VectorPtr<Index_>, const tatami::Options&) const [with OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)0>; tatami::VectorPtr<Index_> = std::shared_ptr<const std::vector >]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:806:68: required from here
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:634:13: 警告：right operand of comma operator has no effect [-Wunused-value]
my_operation,
^~~~~~~~~~~~
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:635:16: 警告：right operand of comma operator has no effect [-Wunused-value]
row,
make: *** [/usr/lib64/R/etc/Makeconf:204：delayed_isometric_binary.o] 错误 1
ERROR: compilation failed for package ‘beachmat’

• removing ‘/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/beachmat’
• restoring previous ‘/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/beachmat’
• installing source package ‘glmGamPoi’ ...
  ** 成功将‘glmGamPoi’程序包解包并MD5和检查
  ** using staged installation
  ** libs
  using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-22)’
  using C++11
  g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include/ -I'/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/RcppArmadillo/include' -I'/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/beachmat/include' -I/usr/local/include -std=c++11 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include/ -I'/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/Rcpp/include' -I'/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/RcppArmadillo/include' -I'/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/beachmat/include' -I/usr/local/include -std=c++11 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c beta_estimation.cpp -o beta_estimation.o
  beta_estimation.cpp:3:10: 致命错误：beachmat/numeric_matrix.h：没有那个文件或目录
  #include "beachmat/numeric_matrix.h"
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
  编译中断。
  make: *** [/usr/lib64/R/etc/Makeconf:204：beta_estimation.o] 错误 1
  ERROR: compilation failed for package ‘glmGamPoi’
• removing ‘/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/glmGamPoi’
• restoring previous ‘/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/glmGamPoi’

下载的程序包在
‘/tmp/Rtmp7vceXl/downloaded_packages’里
Installation paths not writeable, unable to update packages
path: /usr/lib64/R/library
packages:
boot, foreign, MASS, Matrix, nlme, survival
警告信息:
1: In install.packages(...) : 安装程序包‘beachmat’时退出狀態的值不是0
2: In install.packages(...) : 安装程序包‘glmGamPoi’时退出狀態的值不是0

[RenJ-Feng]

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-redhat-linux-gnu
Running under: AlmaLinux 8.10 (Cerulean Leopard)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so; LAPACK version 3.9.0

locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] assorthead_1.0.0 BiocManager_1.30.25 sctransform_0.4.1 SeuratWrappers_0.2.0 ggplot2_3.5.1
[6] patchwork_1.3.0 Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4 dplyr_1.1.4
[11] devtools_2.4.5 usethis_3.0.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9 magrittr_2.0.3 spatstat.utils_3.1-0
[6] farver_2.1.2 fs_1.6.5 vctrs_0.6.5 ROCR_1.0-11 memoise_2.0.1
[11] spatstat.explore_3.3-3 htmltools_0.5.8.1 parallelly_1.38.0 KernSmooth_2.23-24 htmlwidgets_1.6.4
[16] ica_1.0-3 plyr_1.8.9 plotly_4.10.4 zoo_1.8-12 cachem_1.1.0
[21] igraph_2.1.1 mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3 rsvd_1.0.5
[26] Matrix_1.7-0 R6_2.5.1 fastmap_1.2.0 fitdistrplus_1.2-1 future_1.34.0
[31] shiny_1.9.1 digest_0.6.37 colorspace_2.1-1 tensor_1.5 RSpectra_0.16-2
[36] irlba_2.3.5.1 pkgload_1.4.0 progressr_0.15.0 fansi_1.0.6 spatstat.sparse_3.1-0
[41] httr_1.4.7 polyclip_1.10-7 abind_1.4-8 compiler_4.4.1 remotes_2.5.0
[46] withr_3.0.2 fastDummies_1.7.4 pkgbuild_1.4.5 MASS_7.3-60.2 sessioninfo_1.2.2
[51] tools_4.4.1 lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.3 goftest_1.2-3
[56] glue_1.8.0 nlme_3.1-164 promises_1.3.0 grid_4.4.1 Rtsne_0.17
[61] cluster_2.1.6 reshape2_1.4.4 generics_0.1.3 gtable_0.3.6 spatstat.data_3.1-2
[66] tidyr_1.3.1 data.table_1.16.2 utf8_1.2.4 spatstat.geom_3.3-3 RcppAnnoy_0.0.22
[71] ggrepel_0.9.6 RANN_2.6.2 pillar_1.9.0 stringr_1.5.1 spam_2.11-0
[76] RcppHNSW_0.6.0 later_1.3.2 splines_4.4.1 lattice_0.22-6 survival_3.6-4
[81] deldir_2.0-4 tidyselect_1.2.1 miniUI_0.1.1.1 pbapply_1.7-2 gridExtra_2.3
[86] scattermore_1.2 matrixStats_1.4.1 stringi_1.8.4 lazyeval_0.2.2 codetools_0.2-20
[91] tibble_3.2.1 cli_3.6.3 uwot_0.2.2 xtable_1.8-4 reticulate_1.39.0
[96] munsell_0.5.1 Rcpp_1.0.13 globals_0.16.3 spatstat.random_3.3-2 png_0.1-8
[101] spatstat.univar_3.0-1 parallel_4.4.1 ellipsis_0.3.2 dotCall64_1.2 profvis_0.4.0
[106] urlchecker_1.0.1 listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0 ggridges_0.5.6
[111] leiden_0.4.3.1 purrr_1.0.2 rlang_1.1.4 cowplot_1.1.3

[const-ae]

H RenJ,

the issue appears to be that the compilation of beachmat, which is one of glmGamPoi dependencies, fails. I suggest you keep the conversation going with Aaron at tatami-inc/beachmat#34.

Best,
Constantin