Can't install beachmat in almalinux system

[RenJ-Feng]

BiocManager::install("beachmat")
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:608:13: 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:609:16: 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_expanded_internal(bool, tatami::MaybeOracle<oracle_, Index_>, Index_, Index_, const tatami::Options&) const [with bool oracle_ = false; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)6>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::MyopicDenseExtractor<double, int>; tatami::MaybeOracle<oracle_, Index_> = bool]’:
/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_ = false; Args_ = {bool, int&, int&, const tatami::Options&}; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)6>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::MyopicDenseExtractor<double, int>]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:700:37: required from ‘std::unique_ptr<tatami::MyopicDenseExtractor<OutputValue_, Index_> > tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense(bool, Index_, Index_, const tatami::Options&) const [with OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)6>]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:699:66: required from here
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:659:13: 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:660:16: 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:662:24: 警告：right operand of comma operator has no effect [-Wunused-value]
block_start,
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:663:25: 警告：right operand of comma operator has no effect [-Wunused-value]
return std::make_unique<DelayedBinaryIsometricOperation_internal::DenseExpandedBlock<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_simple_internal(bool, tatami::MaybeOracle<oracle_, Index_>, Index_, Index_, const tatami::Options&) const [with bool oracle_ = false; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)6>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::MyopicDenseExtractor<double, int>; tatami::MaybeOracle<oracle_, Index_> = bool]’:
/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_ = false; Args_ = {bool, int&, int&, const tatami::Options&}; OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)6>; typename std::conditional<oracle_, tatami::OracularDenseExtractor<OutputValue_, Index_>, tatami::MyopicDenseExtractor<OutputValue_, Index_> >::type = tatami::MyopicDenseExtractor<double, int>]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:700:37: required from ‘std::unique_ptr<tatami::MyopicDenseExtractor<OutputValue_, Index_> > tatami::DelayedBinaryIsometricOperation<OutputValue_, InputValue_, Index_, Operation_>::dense(bool, Index_, Index_, const tatami::Options&) const [with OutputValue_ = double; InputValue_ = double; Index_ = int; Operation_ = tatami::DelayedBinaryIsometricArithmetic<(tatami::ArithmeticOperation)6>]’
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:699:66: required from here
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:620:13: 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:621:16: 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:623:24: 警告：right operand of comma operator has no effect [-Wunused-value]
block_start,
/home/lenovo/R/x86_64-redhat-linux-gnu-library/4.4/assorthead/include/tatami/isometric/binary/DelayedBinaryIsometricOperation.hpp:624:25: 警告：right operand of comma operator has no effect [-Wunused-value]

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:
In install.packages(...) : 安装程序包‘beachmat’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

[LTLA]

I can't reproduce these compilation warnings, but it's worth noting that even these are just warnings, not errors; I don't see an actual error message in your post.

The warnings don't appear to be correct, either. I suspect that these are false positives from an older version of GCC. I regularly test these C++ libraries with all warnings enabled and I have no issues on GCC 11.4.0.

Session information

R version 4.4.2 Patched (2024-10-31 r87285)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /home/luna/Software/R/R-4-4-branch/lib/libRblas.so 
LAPACK: /home/luna/Software/R/R-4-4-branch/lib/libRlapack.so;  LAPACK version 3.12.0

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

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

other attached packages:
[1] beachmat_2.22.0     BiocManager_1.30.25

loaded via a namespace (and not attached):
 [1] zlibbioc_1.52.0       SparseArray_1.6.0     Matrix_1.7-1         
 [4] lattice_0.22-6        MatrixGenerics_1.18.0 matrixStats_1.4.1    
 [7] abind_1.4-8           S4Arrays_1.6.0        XVector_0.46.0       
[10] BiocGenerics_0.52.0   stats4_4.4.2          IRanges_2.40.0       
[13] grid_4.4.2            DelayedArray_0.32.0   compiler_4.4.2       
[16] tools_4.4.2           Rcpp_1.0.13           S4Vectors_0.44.0     
[19] crayon_1.5.3         

[Yunuuuu]

It cannot be installed in the latest ubuntu: https://github.com/Yunuuuu/BPCellsArray/actions/runs/11802919685/job/32879686391

[LTLA]

You're going to have to give a more informative error message. beachmat builds fine both on my own Ubuntu laptop and on the BioC linux machines.

[Yunuuuu]

Thank you for the quick response. It appears there’s an issue with the R development version on Ubuntu, while the R release version runs smoothly. I’m not very familiar with GitHub Actions, so I’ll run a test for the R development version on my local computer.