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Error during installation of azimuth package due to "dependency ‘presto’ is not available for package ‘Azimuth’" #124

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denvercal1234GitHub opened this issue Sep 19, 2022 · 7 comments
Open

Error during installation of azimuth package due to "dependency ‘presto’ is not available for package ‘Azimuth’" #124

denvercal1234GitHub opened this issue Sep 19, 2022 · 7 comments

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@denvercal1234GitHub
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denvercal1234GitHub commented Sep 19, 2022 •
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Hi there,

I attempted to devtools::install_github("satijalab/azimuth") but encountered the ERROR: dependency ‘presto’ is not available for package ‘Azimuth’ as below (reported also in immunogenomics/presto#16)

Would you mind helping me to address this issue?

Thank you so much.

....
In file included from RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
19 warnings and 3 errors generated.
make: *** [RModularityOptimizer.o] Error 1
ERROR: compilation failed for package ‘Seurat’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Seurat’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Seurat’
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/Rtmp2wOca5/remotes14e346cd65f61/satijalab-azimuth-f3c7904/DESCRIPTION’ ...xit status  
─  preparing ‘Azimuth’:
✔  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
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘Azimuth_0.4.6.tar.gz’
   
ERROR: dependency ‘presto’ is not available for package ‘Azimuth’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Azimuth’
Warning: installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//Rtmp2wOca5/file14e3465eeaf7/Azimuth_0.4.6.tar.gz’ had non-zero exit status

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] bitops_1.0-7           fs_1.5.2               usethis_2.1.6          lubridate_1.8.0        devtools_2.4.4         bit64_4.0.5           
  [7] RcppAnnoy_0.0.19       httr_1.4.4             rprojroot_2.0.3        GenomeInfoDb_1.32.4    backports_1.4.1        tools_4.2.1           
 [13] profvis_0.3.7          utf8_1.2.2             R6_2.5.1               colorspace_2.0-3       rgeos_0.5-9            DBI_1.1.3             
 [19] BiocGenerics_0.42.0    nnet_7.3-17            withr_2.5.0            urlchecker_1.0.1       sp_1.5-0               tidyselect_1.1.2      
 [25] prettyunits_1.1.1      processx_3.7.0         curl_4.3.2             bit_4.0.4              compiler_4.2.1         progressr_0.11.0      
 [31] cli_3.4.0              Biobase_2.56.0         scales_1.2.1           callr_3.7.2            stringr_1.4.1          digest_0.6.29         
 [37] XVector_0.36.0         pkgconfig_2.0.3        htmltools_0.5.3        parallelly_1.32.1      sessioninfo_1.2.2      fastmap_1.1.0         
 [43] htmlwidgets_1.5.4      rlang_1.0.5            rstudioapi_0.14        RSQLite_2.2.17         shiny_1.7.2            generics_0.1.3        
 [49] jsonlite_1.8.0         car_3.1-0              dplyr_1.0.10           RCurl_1.98-1.8         magrittr_2.0.3         modeltools_0.2-23     
 [55] GenomeInfoDbData_1.2.8 Matrix_1.5-1           munsell_0.5.0          Rcpp_1.0.9             S4Vectors_0.34.0       fansi_1.0.3           
 [61] abind_1.4-5            reticulate_1.26        lifecycle_1.0.2        stringi_1.7.8          carData_3.0-5          zlibbioc_1.42.0       
 [67] flexmix_2.3-18         pkgbuild_1.3.1         grid_4.2.1             blob_1.2.3             parallel_4.2.1         listenv_0.8.0         
 [73] promises_1.2.0.1       crayon_1.5.1           miniUI_0.1.1.1         lattice_0.20-45        Biostrings_2.64.1      KEGGREST_1.36.3       
 [79] knitr_1.40             ps_1.7.1               pillar_1.8.1           ggpubr_0.4.0           ggsignif_0.6.3         future.apply_1.9.1    
 [85] codetools_0.2-18       stats4_4.2.1           pkgload_1.3.0          glue_1.6.2             SeuratObject_4.1.1     data.table_1.14.2     
 [91] remotes_2.4.2          png_0.1-7              vctrs_0.4.1            httpuv_1.6.6           tidyr_1.2.1            gtable_0.3.1          
 [97] purrr_0.3.4            assertthat_0.2.1       future_1.28.0          ggplot2_3.3.6.9000     cachem_1.0.6           xfun_0.33             
[103] mime_0.12              broom_1.0.1            xtable_1.8-4           rstatix_0.7.0          later_1.3.0            tibble_3.1.8          
[109] AnnotationDbi_1.58.0   memoise_2.0.1          IRanges_2.30.1         globals_0.16.1         ellipsis_0.3.2         here_1.0.1            
>
@denvercal1234GitHub denvercal1234GitHub mentioned this issue Sep 19, 2022
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@AustinHartman
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It looks like the installation of Seurat also failed. You may want to first begin by installing Seurat on your system with install.packages("Seurat") as it is listed as a suggested package by presto

@denvercal1234GitHub
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Hi @AustinHartman, I:

Restarted R
Remove packages Seurat and SeuratData
Reinstall these 2 packages
Then, install Azimuth package but still encountered the same issue as below.

> detach("package:SeuratData", unload = TRUE)
> detach("package:SeuratObject", unload = TRUE)
Warning message:
‘SeuratObject’ namespace cannot be unloaded:
  namespace ‘SeuratObject’ is imported by ‘Seurat’ so cannot be unloaded 
> detach("package:pbmc3k.SeuratData", unload = TRUE)
> detach("package:Seurat", unload = TRUE)
> remove.packages("Seurat")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
(as ‘lib’ is unspecified)
> install.packages('Seurat')
Error in install.packages : Updating loaded packages

Restarting R session...

> install.packages('Seurat')
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/Seurat_4.1.1.tgz'
Content type 'application/x-gzip' length 3673086 bytes (3.5 MB)
==================================================
downloaded 3.5 MB


The downloaded binary packages are in
	/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmpzLDTLD/downloaded_packages
> remove.packages("SeuratData")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
(as ‘lib’ is unspecified)

Restarting R session...

> devtools::install_github("satijalab/seurat-data")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo satijalab/seurat-data@HEAD
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmpY81YdU/remotes1600a1f24a6a7/satijalab-seurat-data-d6a8ce6/DESCRIPTION’ ...
─  preparing ‘SeuratData’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘SeuratData_0.2.2.tar.gz’
   
* installing *source* package ‘SeuratData’ ...
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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
* DONE (SeuratData)
> devtools::install_github("satijalab/azimuth")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo satijalab/azimuth@HEAD
Downloading GitHub repo immunogenomics/presto@HEAD
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmpY81YdU/remotes1600a64410cbf/immunogenomics-presto-052085d/DESCRIPTION’ ...
─  preparing ‘presto’:
✔  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
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘presto_1.0.0.tar.gz’
   
* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                                                           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                                                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
  static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:645:25: error: no return statement in constexpr function
_LIBCPP_CONSTEXPR _IntT __max_representable_int_for_float() _NOEXCEPT {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
  using _Lim = numeric_limits<_IntT>;
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
    return _Lim::max();
           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
  } else if (__r <= _Lim::lowest()) {
                    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
    return _Lim::min();
           ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:490:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/search.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/concepts:134:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:22:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
abs(const complex<_Tp>& __c)
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
        return abs(__c.real());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
        return abs(__c.imag());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
        __re = abs(__re);
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
    return complex<_Tp>(log(abs(__x)), arg(__x));
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
    return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
                      ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘presto’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/presto’
Warning: installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmpY81YdU/file1600a6aac0304/presto_1.0.0.tar.gz’ had non-zero exit statusDownloading GitHub repo immunogenomics/presto@HEAD
Skipping presto, it is already being installed
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmpY81YdU/remotes1600a6c60d813/satijalab-azimuth-f3c7904/DESCRIPTION’ ...
─  preparing ‘Azimuth’:
✔  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
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘Azimuth_0.4.6.tar.gz’
   
ERROR: dependency ‘presto’ is not available for package ‘Azimuth’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Azimuth’
Warning: installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmpY81YdU/file1600a712a2acc/Azimuth_0.4.6.tar.gz’ had non-zero exit status

@denvercal1234GitHub
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denvercal1234GitHub commented Sep 19, 2022 •
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I now made sure the right version of SeuratData v0.2.2 as advised (#121 ) installed and loaded, but encountered the same error:

Restarting R session...

> library(Seurat)
Attaching SeuratObject
Attaching sp
> library(SeuratData)
── Installed datasets ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── SeuratData v0.2.2 ──
✔ pbmc3k 3.1.4                                                                  

────────────────────────────────────────────────────────────────────────────── Key ──────────────────────────────────────────────────────────────────────────────
✔ Dataset loaded successfully
❯ Dataset built with a newer version of Seurat than installed
❓ Unknown version of Seurat installed

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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     

other attached packages:
[1] pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2        sp_1.5-0                SeuratObject_4.1.1      Seurat_4.1.1           

loaded via a namespace (and not attached):
  [1] backports_1.4.1        plyr_1.8.7             igraph_1.3.4           lazyeval_0.2.2         splines_4.2.1          listenv_0.8.0         
  [7] scattermore_0.8        usethis_2.1.6          GenomeInfoDb_1.32.4    ggplot2_3.3.6.9000     digest_0.6.29          htmltools_0.5.3       
 [13] fansi_1.0.3            magrittr_2.0.3         memoise_2.0.1          tensor_1.5             cluster_2.1.4          ROCR_1.0-11           
 [19] remotes_2.4.2          globals_0.16.1         Biostrings_2.64.1      matrixStats_0.62.0     spatstat.sparse_2.1-1  prettyunits_1.1.1     
 [25] colorspace_2.0-3       rappdirs_0.3.3         blob_1.2.3             ggrepel_0.9.1          dplyr_1.0.10           callr_3.7.2           
 [31] crayon_1.5.1           RCurl_1.98-1.8         jsonlite_1.8.0         spatstat.data_2.2-0    progressr_0.11.0       survival_3.4-0        
 [37] zoo_1.8-11             glue_1.6.2             polyclip_1.10-0        gtable_0.3.1           zlibbioc_1.42.0        XVector_0.36.0        
 [43] leiden_0.4.3           car_3.1-0              pkgbuild_1.3.1         future.apply_1.9.1     BiocGenerics_0.42.0    abind_1.4-5           
 [49] scales_1.2.1           DBI_1.1.3              spatstat.random_2.2-0  rstatix_0.7.0          miniUI_0.1.1.1         Rcpp_1.0.9            
 [55] viridisLite_0.4.1      xtable_1.8-4           spatstat.core_2.4-4    reticulate_1.26        bit_4.0.4              stats4_4.2.1          
 [61] profvis_0.3.7          htmlwidgets_1.5.4      httr_1.4.4             RColorBrewer_1.1-3     modeltools_0.2-23      ellipsis_0.3.2        
 [67] ica_1.0-3              urlchecker_1.0.1       pkgconfig_2.0.3        flexmix_2.3-18         uwot_0.1.14            deldir_1.0-6          
 [73] nnet_7.3-17            utf8_1.2.2             here_1.0.1             reshape2_1.4.4         tidyselect_1.1.2       rlang_1.0.5           
 [79] later_1.3.0            AnnotationDbi_1.58.0   munsell_0.5.0          tools_4.2.1            cachem_1.0.6           cli_3.4.0             
 [85] generics_0.1.3         RSQLite_2.2.17         devtools_2.4.4         broom_1.0.1            ggridges_0.5.3         stringr_1.4.1         
 [91] fastmap_1.1.0          goftest_1.2-3          processx_3.7.0         bit64_4.0.5            fs_1.5.2               fitdistrplus_1.1-8    
 [97] purrr_0.3.4            RANN_2.6.1             KEGGREST_1.36.3        nlme_3.1-159           pbapply_1.5-0          future_1.28.0         
[103] mime_0.12              compiler_4.2.1         rstudioapi_0.14        plotly_4.10.0.9001     png_0.1-7              ggsignif_0.6.3        
[109] spatstat.utils_2.3-1   tibble_3.1.8           stringi_1.7.8          ps_1.7.1               rgeos_0.5-9            lattice_0.20-45       
[115] Matrix_1.5-1           vctrs_0.4.1            pillar_1.8.1           lifecycle_1.0.2        spatstat.geom_2.4-0    lmtest_0.9-40         
[121] RcppAnnoy_0.0.19       data.table_1.14.2      cowplot_1.1.1          bitops_1.0-7           irlba_2.3.5            httpuv_1.6.6          
[127] patchwork_1.1.2        R6_2.5.1               promises_1.2.0.1       gridExtra_2.3          KernSmooth_2.23-20     IRanges_2.30.1        
[133] parallelly_1.32.1      sessioninfo_1.2.2      codetools_0.2-18       MASS_7.3-58.1          assertthat_0.2.1       pkgload_1.3.0         
[139] rprojroot_2.0.3        sctransform_0.3.4      S4Vectors_0.34.0       GenomeInfoDbData_1.2.8 mgcv_1.8-40            parallel_4.2.1        
[145] rpart_4.1.16           grid_4.2.1             tidyr_1.2.1            carData_3.0-5          Rtsne_0.16             ggpubr_0.4.0          
[151] Biobase_2.56.0         shiny_1.7.2            lubridate_1.8.0       
> devtools::install_github("satijalab/azimuth")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo satijalab/azimuth@HEAD
Downloading GitHub repo immunogenomics/presto@HEAD
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmpNk1XHC/remotes161df3ef48092/immunogenomics-presto-052085d/DESCRIPTION’ ...
─  preparing ‘presto’:
✔  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
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘presto_1.0.0.tar.gz’
   
* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                                                           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                                                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
  static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:645:25: error: no return statement in constexpr function
_LIBCPP_CONSTEXPR _IntT __max_representable_int_for_float() _NOEXCEPT {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
  using _Lim = numeric_limits<_IntT>;
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
    return _Lim::max();
           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
  } else if (__r <= _Lim::lowest()) {
                    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
    return _Lim::min();
           ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:490:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/search.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/concepts:134:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:22:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
abs(const complex<_Tp>& __c)
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
        return abs(__c.real());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
        return abs(__c.imag());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
        __re = abs(__re);
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
    return complex<_Tp>(log(abs(__x)), arg(__x));
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
    return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
                      ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘presto’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/presto’
Warning: installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmpNk1XHC/file161df26251188/presto_1.0.0.tar.gz’ had non-zero exit statusDownloading GitHub repo immunogenomics/presto@HEAD
Skipping presto, it is already being installed
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmpNk1XHC/remotes161df602e8db9/satijalab-azimuth-f3c7904/DESCRIPTION’ ...
─  preparing ‘Azimuth’:
✔  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
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘Azimuth_0.4.6.tar.gz’
   
ERROR: dependency ‘presto’ is not available for package ‘Azimuth’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Azimuth’
Warning: installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmpNk1XHC/file161df3414de66/Azimuth_0.4.6.tar.gz’ had non-zero exit status

@AustinHartman
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It's hard to know exactly what the issue is here especially since it's related to an Azimuth dependency rather than Azimuth itself, but my guess is that one or more of presto's dependencies are failing to install which leads to the error. You could try directly installing presto with devtools::install_github("immunogenomics/presto") to see if that gives any additional clues

@denvercal1234GitHub
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Author

Thanks Austin. I:

Restarted R session
Installed presto
Still got the same error

> library(Seurat)
Attaching SeuratObject
Attaching sp
> library(SeuratData)
── Installed datasets ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── SeuratData v0.2.2 ──
✔ pbmc3k 3.1.4                                                                  

────────────────────────────────────────────────────────────────────────────── Key ──────────────────────────────────────────────────────────────────────────────
✔ Dataset loaded successfully
❯ Dataset built with a newer version of Seurat than installed
❓ Unknown version of Seurat installed

> devtools::install_github("immunogenomics/presto")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo immunogenomics/presto@HEAD
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmpT9NN2C/remotes166af310e237d/immunogenomics-presto-052085d/DESCRIPTION’ ...
─  preparing ‘presto’:
✔  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
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘presto_1.0.0.tar.gz’
   
* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                                                           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                                                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
  static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:645:25: error: no return statement in constexpr function
_LIBCPP_CONSTEXPR _IntT __max_representable_int_for_float() _NOEXCEPT {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
  using _Lim = numeric_limits<_IntT>;
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
    return _Lim::max();
           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
  } else if (__r <= _Lim::lowest()) {
                    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
    return _Lim::min();
           ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:490:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/search.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/concepts:134:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:22:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
abs(const complex<_Tp>& __c)
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
        return abs(__c.real());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
        return abs(__c.imag());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
        __re = abs(__re);
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
    return complex<_Tp>(log(abs(__x)), arg(__x));
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
    return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
                      ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘presto’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/presto’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmpT9NN2C/file166af173bfcb4/presto_1.0.0.tar.gz’ had non-zero exit status

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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     

other attached packages:
[1] pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2        sp_1.5-0                SeuratObject_4.1.1      Seurat_4.1.1           

loaded via a namespace (and not attached):
  [1] plyr_1.8.7             igraph_1.3.4           lazyeval_0.2.2         splines_4.2.1          listenv_0.8.0          scattermore_0.8       
  [7] usethis_2.1.6          GenomeInfoDb_1.32.4    ggplot2_3.3.6.9000     digest_0.6.29          htmltools_0.5.3        fansi_1.0.3           
 [13] magrittr_2.0.3         memoise_2.0.1          tensor_1.5             cluster_2.1.4          ROCR_1.0-11            remotes_2.4.2         
 [19] globals_0.16.1         Biostrings_2.64.1      matrixStats_0.62.0     spatstat.sparse_2.1-1  prettyunits_1.1.1      colorspace_2.0-3      
 [25] rappdirs_0.3.3         blob_1.2.3             ggrepel_0.9.1          dplyr_1.0.10           callr_3.7.2            crayon_1.5.1          
 [31] RCurl_1.98-1.8         jsonlite_1.8.0         progressr_0.11.0       spatstat.data_2.2-0    survival_3.4-0         zoo_1.8-11            
 [37] glue_1.6.2             polyclip_1.10-0        gtable_0.3.1           zlibbioc_1.42.0        XVector_0.36.0         leiden_0.4.3          
 [43] pkgbuild_1.3.1         future.apply_1.9.1     BiocGenerics_0.42.0    abind_1.4-5            scales_1.2.1           DBI_1.1.3             
 [49] spatstat.random_2.2-0  miniUI_0.1.1.1         Rcpp_1.0.9             viridisLite_0.4.1      xtable_1.8-4           reticulate_1.26       
 [55] spatstat.core_2.4-4    bit_4.0.4              stats4_4.2.1           profvis_0.3.7          htmlwidgets_1.5.4      httr_1.4.4            
 [61] RColorBrewer_1.1-3     modeltools_0.2-23      ellipsis_0.3.2         ica_1.0-3              urlchecker_1.0.1       pkgconfig_2.0.3       
 [67] flexmix_2.3-18         uwot_0.1.14            deldir_1.0-6           nnet_7.3-17            utf8_1.2.2             here_1.0.1            
 [73] tidyselect_1.1.2       rlang_1.0.5            reshape2_1.4.4         later_1.3.0            AnnotationDbi_1.58.0   munsell_0.5.0         
 [79] tools_4.2.1            cachem_1.0.6           cli_3.4.0              generics_0.1.3         RSQLite_2.2.17         devtools_2.4.4        
 [85] ggridges_0.5.3         stringr_1.4.1          fastmap_1.1.0          goftest_1.2-3          processx_3.7.0         bit64_4.0.5           
 [91] fs_1.5.2               fitdistrplus_1.1-8     purrr_0.3.4            RANN_2.6.1             KEGGREST_1.36.3        nlme_3.1-159          
 [97] pbapply_1.5-0          future_1.28.0          mime_0.12              compiler_4.2.1         rstudioapi_0.14        plotly_4.10.0.9001    
[103] curl_4.3.2             png_0.1-7              spatstat.utils_2.3-1   tibble_3.1.8           stringi_1.7.8          ps_1.7.1              
[109] rgeos_0.5-9            lattice_0.20-45        Matrix_1.5-1           vctrs_0.4.1            pillar_1.8.1           lifecycle_1.0.2       
[115] spatstat.geom_2.4-0    lmtest_0.9-40          RcppAnnoy_0.0.19       data.table_1.14.2      cowplot_1.1.1          bitops_1.0-7          
[121] irlba_2.3.5            httpuv_1.6.6           patchwork_1.1.2        R6_2.5.1               promises_1.2.0.1       KernSmooth_2.23-20    
[127] gridExtra_2.3          IRanges_2.30.1         parallelly_1.32.1      sessioninfo_1.2.2      codetools_0.2-18       MASS_7.3-58.1         
[133] assertthat_0.2.1       pkgload_1.3.0          rprojroot_2.0.3        withr_2.5.0            sctransform_0.3.4      S4Vectors_0.34.0      
[139] GenomeInfoDbData_1.2.8 mgcv_1.8-40            parallel_4.2.1         rpart_4.1.16           grid_4.2.1             tidyr_1.2.1           
[145] Rtsne_0.16             Biobase_2.56.0         shiny_1.7.2            lubridate_1.8.0

@AustinHartman
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Sorry that did not work, it is tricky to offer guidance since this is a local build issue. Perhaps you could check xcode command line tools are properly installed and make sure you are using an install of R from CRAN rather than conda or brew

@ClarisseGanier
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I fixed it by installing "BSgenome.Hsapiens.UCSC.hg38" separately using :
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

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@AustinHartman @denvercal1234GitHub @ClarisseGanier