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Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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installation of package ‘HDF5Array’ had non-zero exit status #60

Closed mick42-star closed 8 months ago

mick42-star commented 8 months ago

Hi, I am trying to install HDF6Array on a Mac M2 chip, and ran into some errors.

R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.0

BiocManager::install("HDF5Array") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Installing package(s) 'HDF5Array' Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘HDF5Array’ Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source package ‘HDF5Array’

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/HDF5Array_1.30.0.tar.gz' Content type 'application/x-gzip' length 8098331 bytes (7.7 MB)

downloaded 7.7 MB

The downloaded source packages are in ‘/private/var/folders/04/vxdd83rj7ks4fy1nxcx9rf3c0000gn/T/Rtmp5WTUEb/downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘HDF5Array’ had non-zero exit status

library(crypto) Loading required package: rvest Loading required package: xml2 BiocManager::install("HDF5Array") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Installing package(s) 'HDF5Array' Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘HDF5Array’ Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source package ‘HDF5Array’

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/HDF5Array_1.30.0.tar.gz' Content type 'application/x-gzip' length 8098331 bytes (7.7 MB)

downloaded 7.7 MB

The downloaded source packages are in ‘/private/var/folders/04/vxdd83rj7ks4fy1nxcx9rf3c0000gn/T/Rtmp5WTUEb/downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘HDF5Array’ had non-zero exit status

vjcitn commented 8 months ago

plz provide sessionInfo() output after error and verify BiocManager::valid() is TRUE

mick42-star commented 8 months ago

plz provide sessionInfo() output after error and verify BiocManager::valid() is TRUE

sessionInfo() R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.0

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

loaded via a namespace (and not attached): [1] miniUI_0.1.1.1 compiler_4.3.1 BiocManager_1.30.22 crayon_1.5.2 promises_1.2.1
[6] Rcpp_1.0.11 stringr_1.5.0 callr_3.7.3 later_1.3.1 fastmap_1.1.1
[11] mime_0.12 R6_2.5.1 curl_5.1.0 htmlwidgets_1.6.2 desc_1.4.2
[16] profvis_0.3.8 rprojroot_2.0.3 shiny_1.7.5.1 rlang_1.1.1 cachem_1.0.8
[21] stringi_1.7.12 httpuv_1.6.12 fs_1.6.3 pkgload_1.3.3 memoise_2.0.1
[26] cli_3.6.1 magrittr_2.0.3 ps_1.7.5 digest_0.6.33 processx_3.8.2
[31] rstudioapi_0.15.0 xtable_1.8-4 remotes_2.4.2.1 devtools_2.4.5 lifecycle_1.0.3
[36] prettyunits_1.2.0 vctrs_0.6.4 glue_1.6.2 urlchecker_1.0.1 sessioninfo_1.2.2
[41] pkgbuild_1.4.2 purrr_1.0.2 usethis_2.2.2 tools_4.3.1 ellipsis_0.3.2
[46] htmltools_0.5.6.1

BiocManager::valid() 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/

R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.0

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

loaded via a namespace (and not attached): [1] miniUI_0.1.1.1 compiler_4.3.1 BiocManager_1.30.22 crayon_1.5.2 promises_1.2.1
[6] Rcpp_1.0.11 stringr_1.5.0 callr_3.7.3 later_1.3.1 fastmap_1.1.1
[11] mime_0.12 R6_2.5.1 curl_5.1.0 htmlwidgets_1.6.2 desc_1.4.2
[16] profvis_0.3.8 rprojroot_2.0.3 shiny_1.7.5.1 rlang_1.1.1 cachem_1.0.8
[21] stringi_1.7.12 httpuv_1.6.12 fs_1.6.3 pkgload_1.3.3 memoise_2.0.1
[26] cli_3.6.1 magrittr_2.0.3 ps_1.7.5 digest_0.6.33 processx_3.8.2
[31] rstudioapi_0.15.0 xtable_1.8-4 remotes_2.4.2.1 devtools_2.4.5 lifecycle_1.0.3
[36] prettyunits_1.2.0 vctrs_0.6.4 glue_1.6.2 urlchecker_1.0.1 sessioninfo_1.2.2
[41] pkgbuild_1.4.2 purrr_1.0.2 usethis_2.2.2 tools_4.3.1 ellipsis_0.3.2
[46] htmltools_0.5.6.1

Bioconductor version '3.18'

create a valid installation with

BiocManager::install(c( "enrichplot", "htmltools" ), update = TRUE, ask = FALSE, force = TRUE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message: 1 packages out-of-date; 1 packages too new

hpages commented 8 months ago

@mick42-star It looks to me that you are missing the crypto library which you can get by downloading and installing the precompiled openssl binary from https://mac.r-project.org/bin/ Make sure to grab the binary for your architecture.

Note that https://mac.r-project.org/bin/ is the first place you should check when missing libraries on your Mac. In particular, it is not recommended to install things via Homebrew, which is known to be a potential source of problems in the context of installing/compiling R or R packages.

Alternatively, a binary version of the HDF5Array package will become available for Mac arm64 in the next couple of days, so you could wait for that.

Best, H.

ronfinn commented 8 months ago

I have had a similar install error :

> BiocManager::install("HDF5Array")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'HDF5Array'
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: 'HDF5Array'
Do you want to attempt to install these from sources? (Yes/no/cancel) 
installing the source package 'HDF5Array'

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/HDF5Array_1.30.0.tar.gz'
Content type 'application/x-gzip' length 8098331 bytes (7.7 MB)
==================================================
downloaded 7.7 MB

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
using C compiler: ‘gcc-13 (Homebrew GCC 13.2.0) 13.2.0’
using SDK: ‘’
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c H5File.c -o H5File.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c global_errmsg_buf.c -o global_errmsg_buf.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5dimscales.c -o h5dimscales.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c uaselection.c -o uaselection.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_helpers.c -o h5mread_helpers.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_startscounts.c -o h5mread_startscounts.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ChunkIterator.c -o ChunkIterator.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_index.c -o h5mread_index.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: 'NOT_USED_make_nzindex_from_bufs' defined but not used [-Wunused-function]
  206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: 'NOT_USED_make_nzdata_from_IntAE_bufs' defined but not used [-Wunused-function]
  179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: 'NOT_USED_make_nzindex_from_buf' defined but not used [-Wunused-function]
  123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread.c -o h5mread.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5summarize.c -o h5summarize.o
/opt/homebrew/bin/gcc-13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
/opt/homebrew/bin/gcc-13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5_hl.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library not found for -lcrypto
collect2: error: ld returned 1 exit status
make: *** [HDF5Array.so] Error 1
ERROR: compilation failed for package ‘HDF5Array’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/HDF5Array’

The downloaded source packages are in
    '/private/var/folders/04/jw8n0g8j29d6gdvcqwjjlp740000gq/T/RtmpTqQD6U/downloaded_packages'
Warning message:
In install.packages(...) :
  installation of package 'HDF5Array' had non-zero exit status

I spent some time to solve the error to no avail. Any suggestions on how to fix this?

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] dotCall64_1.1-0         fastmatch_1.1-4         gtable_0.3.4           
 [4] spam_2.10-0             ggplot2_3.4.4           RcppRoll_0.3.0         
 [7] lattice_0.22-5          vctrs_0.6.4             tools_4.3.2            
[10] bitops_1.0-7            generics_0.1.3          stats4_4.3.2           
[13] parallel_4.3.2          tibble_3.2.1            fansi_1.0.5            
[16] pkgconfig_2.0.3         Matrix_1.6-1.1          data.table_1.14.8      
[19] S4Vectors_0.40.1        lifecycle_1.0.3         GenomeInfoDbData_1.2.11
[22] farver_2.1.1            compiler_4.3.2          Rsamtools_2.18.0       
[25] Biostrings_2.70.1       munsell_0.5.0           ggforce_0.4.1          
[28] codetools_0.2-19        SeuratObject_5.0.0      GenomeInfoDb_1.38.0    
[31] RCurl_1.98-1.13         pillar_1.9.0            crayon_1.5.2           
[34] tidyr_1.3.0             MASS_7.3-60             BiocParallel_1.36.0    
[37] parallelly_1.36.0       tidyselect_1.2.0        digest_0.6.33          
[40] stringi_1.7.12          future_1.33.0           dplyr_1.1.3            
[43] purrr_1.0.2             listenv_0.9.0           polyclip_1.10-6        
[46] grid_4.3.2              colorspace_2.1-0        cli_3.6.1              
[49] magrittr_2.0.3          patchwork_1.1.3         utf8_1.2.4             
[52] future.apply_1.11.0     withr_2.5.2             scales_1.2.1           
[55] sp_2.1-1                XVector_0.42.0          globals_0.16.2         
[58] progressr_0.14.0        pbapply_1.7-2           GenomicRanges_1.54.1   
[61] IRanges_2.36.0          irlba_2.3.5.1           rlang_1.1.2            
[64] Rcpp_1.0.11             glue_1.6.2              tweenr_2.0.2           
[67] Signac_1.12.9001        BiocGenerics_0.48.1     rstudioapi_0.15.0      
[70] R6_2.5.1                zlibbioc_1.48.0        
>
LiNk-NY commented 8 months ago

Hi Ron, @ronfinn It looks like the same advice applies to your version of openssl on Mac. Please install a compatible binary from https://mac.r-project.org/bin/. Best, Marcel

mick42-star commented 8 months ago

@mick42-star It looks to me that you are missing the crypto library which you can get by downloading and installing the precompiled openssl binary from https://mac.r-project.org/bin/ Make sure to grab the binary for your architecture.

Note that https://mac.r-project.org/bin/ is the first place you should check when missing libraries on your Mac. In particular, it is not recommended to install things via Homebrew, which is known to be a potential source of problems in the context of installing/compiling R or R packages.

Alternatively, a binary version of the HDF5Array package will become available for Mac arm64 in the next couple of days, so you could wait for that.

Best, H.

Hi, with the link https://mac.r-project.org/bin/ , I wasn't able to find the library for crypto. Maybe I will just wait for binary version of the HDF5Array package. Thanks!

hpages commented 8 months ago

@mick42-star As mentioned above, the crypto library should be part of the precompiled openssl binary from https://mac.r-project.org/bin/. Did you try that?

ronfinn commented 8 months ago

It worked! absolute legends. Thank you all! https://mac.r-project.org/bin/ is a nice find and will probably save me in the future.

mick42-star commented 8 months ago

precompiled

install.libs("openssl") Downloading https://mac.R-project.org/bin/REPOS ... Using repository https://mac.R-project.org/bin/darwin20/arm64 ... Downloading index https://mac.R-project.org/bin/darwin20/arm64/PACKAGES ... Downloading + installing https://mac.R-project.org/bin/darwin20/arm64/openssl-1.1.1t-darwin.20-arm64.tar.xz ...

I installed openssl, but the problem still exists

mainyanghr commented 8 months ago

I have the same issues and still can not solve the problems. Please help! I have been struggling with package installation for single cell analysis on my M1 chip MacBook . In order to install Azimuth package, I need to install the glmGamPoi that also needs the HDF5Array package. I read your suggestions online from Github for M1 computer, but it is still not working. Any comments are welcome! Could someone give a cleaner instructions how to use the install. libs and openssl.

> sessionInfo() '''''''''''''''''''''' R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.3.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] openssl_2.1.1

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7
[4] magrittr_2.0.3 spatstat.utils_3.0-4 rmarkdown_2.25

**source("https://mac.R-project.org/bin/install.R") install.libs("openssl") library(openssl)

install.libs("HDF5Array")

install.libs(pkgs = "/Users/Desktop/Lab work/Lynch project/Results/Code/database/HDF5Array_1.30.0.tgz" ''''''''''''''''''''''''''' > install.libs("HDF5Array")** Downloading https://mac.R-project.org/bin/REPOS ... Using repository https://mac.R-project.org/bin/darwin20/arm64 ... Downloading index https://mac.R-project.org/bin/darwin20/arm64/PACKAGES ... Error in deps(pkgs, db) : Following binaries have no download candidates: HDF5Array

mainyanghr commented 8 months ago

precompiled

install.libs("openssl") Downloading https://mac.R-project.org/bin/REPOS ... Using repository https://mac.R-project.org/bin/darwin20/arm64 ... Downloading index https://mac.R-project.org/bin/darwin20/arm64/PACKAGES ... Downloading + installing https://mac.R-project.org/bin/darwin20/arm64/openssl-1.1.1t-darwin.20-arm64.tar.xz ...

I installed openssl, but the problem still exists

Me too. I installed openssl, the HDF5Array is still not able to be installed by trying install.libs("HDF5Array") or install.libs(pkgs = "/Users/Desktop/Lab work/project/Results/Code/database/HDF5Array_1.30.0.tgz

hpages commented 8 months ago

@mainyanghr Always use BiocManager::install() to install a Bioconductor package. install.libs() is a small dedicated utility provided by Simon Urbanek for downloading and installing the precompiled libraries that he makes and hosts at mac.r-project.org.

hpages commented 8 months ago

@mick42-star Are you sure it's the same error? Can you show the output of ls -l /opt/R/arm64/lib/? (command to execute at the Unix command line)

Also FWIW it's probably a good idea to try BiocManager::install("HDF5Array") in a fresh R session, and not in the same session where you did install.libs("openssl"). Maybe you did that already, I don't know.

Anyways, can you try this again in a fresh session and show the exact command you used + its full output + your sessionInfo() again? With an effort to properly format the whole thing if it's not asking too much.

Thanks, H.

P.S.: GitHub issue tracker supports markdown and a good practice is to use that feature to make your messages easier to read for everybody. For example by putting a line with 3 backticks before and after the code that you copy/paste in your messages. It's also good practice to do this for the output of commands. That advice is also for you @mainyanghr. Thanks!

mick42-star commented 8 months ago

BiocManager::install("HDF5Array")

Sorry, I was doing BiocManager::install("HDF5Array") in Rstudio instead of R console. It works now. Many thanks.