NetPathMiner Fails to Install through Bioconductor on Mac Sonoma 14.2

[margot-l]

The Bug

When I try and install NetPath Miner through Bioconductor or through GitHub, compilation fails because PathRanker.cpp:27:10: fatal error: 'boost/graph/graph_utility.hpp' file not found. I have made sure that Boost is updated through Homebrew.

To Reproduce

1. Have libSMBL downloaded according to instructions.
2. Try to install NetPathMiner in RStudio either via BioConductor or devtools.
3. See error.

 if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install("NetPathMiner")  
installing the source package ‘NetPathMiner’

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/NetPathMiner_1.38.0.tar.gz'
Content type 'application/x-gzip' length 2718683 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
Non x86_64 architecture. Using system-wide boost installation!
libSBML found, finding configuration...
pkg-config tool found
Couldn't find libsbml.pc. Searching for libsbml in candidate directories.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX14.0.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DHAVE_SBML -I/usr/local/include/  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
PathRanker.cpp:27:10: fatal error: 'boost/graph/graph_utility.hpp' file not found
#include <boost/graph/graph_utility.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [PathRanker.o] Error 1
ERROR: compilation failed for package ‘NetPathMiner’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/NetPathMiner’

Installing with Devtools through Github

> library(devtools)   
> install_github(repo="ahmohamed/NetPathMiner")
Downloading GitHub repo ahmohamed/NetPathMiner@HEAD
── R CMD build ───────────────────────────────────
✔  checking for file ‘/private/var/folders/qq/3f83nkd158n0nkw_6t58h_cw0000gq/T/Rtmpq5tCj2/remotesb09e28859697/ahmohamed-NetPathMiner-45653d1/DESCRIPTION’ ...
─  preparing ‘NetPathMiner’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  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 ‘NetPathMiner_1.37.0.tar.gz’
   
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
Non x86_64 architecture. Using system-wide boost installation!
libSBML found, finding configuration...
pkg-config tool found
Couldn't find libsbml.pc. Searching for libsbml in candidate directories.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX14.0.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DHAVE_SBML -I/usr/local/include/  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
PathRanker.cpp:27:10: fatal error: 'boost/graph/graph_utility.hpp' file not found
#include <boost/graph/graph_utility.hpp>
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [PathRanker.o] Error 1
ERROR: compilation failed for package ‘NetPathMiner’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/NetPathMiner’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/qq/3f83nkd158n0nkw_6t58h_cw0000gq/T//Rtmpq5tCj2/fileb09e4719d6e7/NetPathMiner_1.37.0.tar.gz’ had non-zero exit status

My sessionInfo()

R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.2

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

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rounding 
 
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/Toronto
tzcode source: internal

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

other attached packages:
[1] devtools_2.4.5  dtwclust_5.5.12
[3] dtw_1.23-1      usethis_2.2.2  
[5] biomaRt_2.58.0  proxy_0.4-27   

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     
  [2] rstudioapi_0.15.0      
  [3] magrittr_2.0.3         
  [4] modeltools_0.2-23      
  [5] fs_1.6.3               
  [6] zlibbioc_1.48.0        
  [7] vctrs_0.6.4            
  [8] memoise_2.0.1          
  [9] RCurl_1.98-1.13        
 [10] htmltools_0.5.7        
 [11] forcats_1.0.0          
 [12] progress_1.2.2         
 [13] curl_5.1.0             
 [14] desc_1.4.2             
 [15] htmlwidgets_1.6.3      
 [16] plyr_1.8.9             
 [17] cachem_1.0.8           
 [18] igraph_1.5.1           
 [19] mime_0.12              
 [20] lifecycle_1.0.4        
 [21] iterators_1.0.14       
 [22] pkgconfig_2.0.3        
 [23] Matrix_1.6-4           
 [24] R6_2.5.1               
 [25] fastmap_1.1.1          
 [26] GenomeInfoDbData_1.2.11
 [27] shiny_1.8.0            
 [28] clue_0.3-65            
 [29] digest_0.6.33          
 [30] colorspace_2.1-0       
 [31] rARPACK_0.11-0         
 [32] ps_1.7.5               
 [33] AnnotationDbi_1.64.1   
 [34] S4Vectors_0.40.2       
 [35] rprojroot_2.0.4        
 [36] RSpectra_0.16-1        
 [37] pkgload_1.3.3          
 [38] ellipse_0.5.0          
 [39] RSQLite_2.3.3          
 [40] filelock_1.0.2         
 [41] fansi_1.0.5            
 [42] httr_1.4.7             
 [43] compiler_4.3.0         
 [44] remotes_2.4.2.1        
 [45] bit64_4.0.5            
 [46] BiocParallel_1.36.0    
 [47] DBI_1.1.3              
 [48] pkgbuild_1.4.2         
 [49] MASS_7.3-60            
 [50] sessioninfo_1.2.2      
 [51] rappdirs_0.3.3         
 [52] corpcor_1.6.10         
 [53] tools_4.3.0            
 [54] httpuv_1.6.12          
 [55] flexclust_1.4-1        
 [56] glue_1.6.2             
 [57] callr_3.7.3            
 [58] promises_1.2.1         
 [59] gridtext_0.1.5         
 [60] grid_4.3.0             
 [61] cluster_2.1.5          
 [62] reshape2_1.4.4         
 [63] generics_0.1.3         
 [64] gtable_0.3.4           
 [65] class_7.3-22           
 [66] tidyr_1.3.0            
 [67] hms_1.1.3              
 [68] xml2_1.3.5             
 [69] utf8_1.2.4             
 [70] XVector_0.42.0         
 [71] BiocGenerics_0.48.1    
 [72] ggrepel_0.9.4          
 [73] foreach_1.5.2          
 [74] pillar_1.9.0           
 [75] stringr_1.5.1          
 [76] later_1.3.1            
 [77] dplyr_1.1.4            
 [78] ggtext_0.1.2           
 [79] BiocFileCache_2.10.1   
 [80] lattice_0.22-5         
 [81] bit_4.0.5              
 [82] tidyselect_1.2.0       
 [83] mixOmics_6.26.0        
 [84] Biostrings_2.70.1      
 [85] miniUI_0.1.1.1         
 [86] gridExtra_2.3          
 [87] IRanges_2.36.0         
 [88] stats4_4.3.0           
 [89] Biobase_2.62.0         
 [90] matrixStats_1.1.0      
 [91] stringi_1.8.2          
 [92] evaluate_0.23          
 [93] codetools_0.2-19       
 [94] tibble_3.2.1           
 [95] cli_3.6.1              
 [96] RcppParallel_5.1.7     
 [97] xtable_1.8-4           
 [98] processx_3.8.2         
 [99] munsell_0.5.0          
[100] Rcpp_1.0.11            
[101] GenomeInfoDb_1.38.1    
[102] dbplyr_2.4.0           
[103] png_0.1-8              
[104] XML_3.99-0.16          
[105] parallel_4.3.0         
[106] ellipsis_0.3.2         
[107] ggh4x_0.2.6            
[108] ggplot2_3.4.4          
[109] blob_1.2.4             
[110] prettyunits_1.2.0      
[111] profvis_0.3.8          
[112] urlchecker_1.0.1       
[113] bitops_1.0-7           
[114] ggthemes_5.0.0         
[115] scales_1.3.0           
[116] purrr_1.0.2            
[117] crayon_1.5.2           
[118] rlang_1.1.2            
[119] KEGGREST_1.42.0        
[120] shinyjs_2.1.0 
```