Installation failure

[zhiiiyang]

Hi @patrickjdanaher, I am having problems with installing this package on my MacBook. I used devtools::install_github("Nanostring-Biostats/InSituType", dependencies = TRUE).

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        compiler_4.2.0    later_1.3.0       urlchecker_1.0.1  prettyunits_1.1.1 profvis_0.3.7    
 [7] remotes_2.4.2     tools_4.2.0       digest_0.6.29     pkgbuild_1.3.1    pkgload_1.3.0     memoise_2.0.1    
[13] lifecycle_1.0.3   rlang_1.0.6       shiny_1.7.2       cli_3.4.1         rstudioapi_0.13   curl_4.3.2       
[19] fastmap_1.1.0     withr_2.5.0       stringr_1.4.1     fs_1.5.2          htmlwidgets_1.5.4 devtools_2.4.4   
[25] rprojroot_2.0.3   glue_1.6.2        R6_2.5.1          processx_3.7.0    sessioninfo_1.2.2 callr_3.7.2      
[31] purrr_0.3.4       magrittr_2.0.3    ps_1.7.1          promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.3  
[37] usethis_2.1.6     mime_0.12         xtable_1.8-4      httpuv_1.6.5      stringi_1.7.8     miniUI_0.1.1.1   
[43] cachem_1.0.6      crayon_1.5.2    

[davidpross]

Hi @zhiiiyang, thanks for the heads up. It looks like it might be an issue with compiling the Rcpp part of the package on a MacBook with Apple Silicon. I will test it with my personal laptop and let you know what I find.

[davidpross]

I got this error also @zhiiiyang. It appears to be a common error when installing packages that use Rcpp on Macs with Apple Silicon. I was able to solve it on my machine by following the instructions here.

You probably already have the Xcode tools, so look over the GNU Fortran section and the Apple silicon Macs subsection.

Let me know if that works for you.

[zhiiiyang]

It worked! Thank you, @davidpross.

[joaolsf]

Hi, I get the exact same error, even after installing Xcode and GNU Fortran following the instructions in the link in your comment @davidpross

devtools::install_github("https://github.com/Nanostring-Biostats/InSituType") Downloading GitHub repo Nanostring-Biostats/InSituType@HEAD Skipping 3 packages not available: SingleCellExperiment, SummarizedExperiment, sparseMatrixStats ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/0m/4rwt_z816mlcps48xsc34jvc0000gn/T/RtmpIzlMP7/remotesea05a67a7ad/Nanostring-Biostats-InSituType-0834eaf/DESCRIPTION’ ... ─ preparing ‘InSituType’: ✔ 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 ─ building ‘InSituType_1.0.0.tar.gz’

• installing source package ‘InSituType’ ... using staged installation libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++11 using SDK: ‘MacOSX13.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpparma_dnbinom_sparse.cpp -o rcpparma_dnbinom_sparse.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o InSituType.so RcppExports.o rcpparma_dnbinom_sparse.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-InSituType/00new/InSituType/libs R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘lsa’ Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘InSituType’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/InSituType’ Warning message: In i.p(...) : installation of package ‘/var/folders/0m/4rwt_z816mlcps48xsc34jvc0000gn/T//RtmpIzlMP7/fileea04b317d39/InSituType_1.0.0.tar.gz’ had non-zero exit status

[limin321]

here

Hi, I have a macOS Monterey with Apple M2 chip. Following the instruction, I installed Xcode and GNU Fortran compiler. When I try to install the Mandatory libraries, I ran into errors in R. Here is my codes.

source("https://mac.R-project.org/bin/install.R")
install.libs("r-base-dev")

Here is my Mac information:

Any suggestion on how to solve this issue?

Thanks. LC

[davidpross]

@limin321 it looks like you may be running into a permissions issue, see this note from the r-project page:

NOTE: if you don't have write-permission in the installation location, you may need to make it writable or run sudo R.

What installation error do you get when you try to install InSituType?

[yubin-ai]

I was able to solve my issues with:

1. install Gnu from https://mac.r-project.org/tools/
2. install.packages("lsa")

[oospina]

Hello, I recently installed Insitutype on two different machines, and it failed because:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘lsa’ Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted

The installation went without issues after install.packages('lsa'). Should lsa be added to DESCRIPTION?