installation error - package or namespace load failed

[agalychnica]

Hi,
I'm trying to install the MicrobiomeAnalyst package in my laptop and after a lot of warnings I get an error

package or namespace load failed for ‘MicrobiomeAnalystR’ in namespaceExport(ns, exports):
 undefined exports: CreateFooter, CreateMDPRnwReport, CreateRHistAppendix, CreateSDPRnwReport, PreparePDFReport
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/private/var/folders/0m/3b5s367d4672dgm3snm3m2nst2fz4v/T/RtmplmZazy/Rinst99e4c8b6500/MicrobiomeAnalystR’
      -----------------------------------
ERROR: package installation failed

I'm using a Mac Apple M3Max, running macOS Sonoma 14.6.1, with latest versions of R and RStudio.
I reinstalled gfortran and a series of things that were initially coming up as errors, and after all that, it gives me large error message (attached as a file here) and which ends in the message that I pasted above.

Can you point me into how I could fix this issue?

Thanks

Below I copy/paste the log of what I got when trying to compile from the git cloned repository:

$ R CMD build MicrobiomeAnalystR

* checking for file ‘MicrobiomeAnalystR/DESCRIPTION’ ... OK
* preparing ‘MicrobiomeAnalystR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘MicrobiomeAnalystR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
Warning: /opt/gfortran/SDK is invalid, setting SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
  Consider running the following to fix (or set SDKROOT):
  ln -sfn /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk /opt/gfortran/SDK
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘’
rm -f init.o rowttests.o util.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rowttests.c -o rowttests.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c util.c -o util.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MicrobiomeAnalystR.so init.o rowttests.o util.o -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
installing to /private/var/folders/0m/3b5s367d4672dgm3snm3m2nst2fz4v/T/RtmplmZazy/Rinst99e4c8b6500/00LOCK-MicrobiomeAnalystR/00new/MicrobiomeAnalystR/libs
** R
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘MASS::area’ by ‘genefilter::area’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::ring’ by ‘igraph::ring’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::edges’ by ‘igraph::edges’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::mst’ by ‘igraph::mst’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::degree’ by ‘igraph::degree’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::complement’ by ‘metacoder::complement’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘igraph::hierarchy’ by ‘metacoder::hierarchy’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ggplot2::map_data’ by ‘metacoder::map_data’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘edgeR::calcNormFactors’ by ‘metagenomeSeq::calcNormFactors’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::filter_taxa’ by ‘phyloseq::filter_taxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘gridExtra::combine’ by ‘randomForest::combine’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape::melt’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_root’ by ‘taxa::is_root’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_stem’ by ‘taxa::is_stem’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘igraph::as_data_frame’ by ‘taxa::as_data_frame’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::n_subtaxa’ by ‘taxa::n_subtaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_internode’ by ‘taxa::is_internode’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxon’ by ‘taxa::taxon’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::internodes’ by ‘taxa::internodes’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxon_id’ by ‘taxa::taxon_id’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::subtaxa’ by ‘taxa::subtaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::n_supertaxa’ by ‘taxa::n_supertaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxon_rank’ by ‘taxa::taxon_rank’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::stems’ by ‘taxa::stems’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::leaves’ by ‘taxa::leaves’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::n_leaves’ by ‘taxa::n_leaves’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::roots’ by ‘taxa::roots’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxonomy’ by ‘taxa::taxonomy’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::supertaxa’ by ‘taxa::supertaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_leaf’ by ‘taxa::is_leaf’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘igraph::diversity’ by ‘vegan::diversity’ when loading ‘MicrobiomeAnalystR’
Note: possible error in 'select(sample_id, everything())': unused argument (everything()) 
Note: possible error in 'layout(xaxis = ax, yaxis = ax)': unused arguments (xaxis = ax, yaxis = ax) 
Note: possible error in 'MicIDmap(predModel = "gem", ': unused argument (predModel = "gem") 
Note: possible error in 'PerformPairDEAnalyse(NA, ': unused arguments (overlay = "T", initDE = "0", adjustedVar = NULL) 
Note: possible error in 'data.frame(sample_data(mbSet$dataSet$proc.phyobj), ': formal argument "check.names" matched by multiple actual arguments 
Note: possible error in 'layout(margin = list(l = 20, ': unused argument (margin = list(l = 20, r = 20, b = 20, t = 40)) 
Note: possible error in 'layout(ggplotly(p, width = 800, ': unused arguments (autosize = FALSE, margin = mbSetObj$imgSet$margin.config) 
Note: possible error in 'layout(ggplotly(p, width = 800, ': unused arguments (autosize = FALSE, margin = mbSetObj$imgSet$margin.config) 
Note: possible error in 'layout(title = plot_data$data$layout$title, ': unused arguments (title = plot_data$data$layout$title, xaxis = plot_data$layout$xaxis, yaxis = plot_data$layout$yaxis, shapes = plot_data$layout$shapes, annotations = plot_data$annotations, note = "proc") 
Note: possible error in 'layout(xaxis = ax, yaxis = ax)': unused arguments (xaxis = ax, yaxis = ax) 
Note: possible error in 'layout(note = "stack")': unused argument (note = "stack") 
Note: possible error in 'layout(title = "", xaxis = list(showgrid = FALSE, ': unused arguments (title = "", xaxis = list(showgrid = FALSE, zeroline = FALSE, showticklabels = FALSE), yaxis = list(showgrid = FALSE, zeroline = FALSE, showticklabels = FALSE)) 
Note: possible error in 'ComputeColorGradient(as.numeric(vec), ': unused arguments (F, F) 
Note: possible error in 'gg_color_hue(length(unique(meta.vec)), ': unused argument ("green") 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘MASS::area’ by ‘genefilter::area’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::ring’ by ‘igraph::ring’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::edges’ by ‘igraph::edges’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::mst’ by ‘igraph::mst’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::degree’ by ‘igraph::degree’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ape::complement’ by ‘metacoder::complement’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘igraph::hierarchy’ by ‘metacoder::hierarchy’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ggplot2::map_data’ by ‘metacoder::map_data’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘edgeR::calcNormFactors’ by ‘metagenomeSeq::calcNormFactors’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::filter_taxa’ by ‘phyloseq::filter_taxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘gridExtra::combine’ by ‘randomForest::combine’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘data.table::melt’ by ‘reshape::melt’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_root’ by ‘taxa::is_root’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_stem’ by ‘taxa::is_stem’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘igraph::as_data_frame’ by ‘taxa::as_data_frame’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::n_subtaxa’ by ‘taxa::n_subtaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_internode’ by ‘taxa::is_internode’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxon’ by ‘taxa::taxon’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::internodes’ by ‘taxa::internodes’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxon_id’ by ‘taxa::taxon_id’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::subtaxa’ by ‘taxa::subtaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::n_supertaxa’ by ‘taxa::n_supertaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxon_rank’ by ‘taxa::taxon_rank’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::stems’ by ‘taxa::stems’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::leaves’ by ‘taxa::leaves’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::n_leaves’ by ‘taxa::n_leaves’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::roots’ by ‘taxa::roots’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::taxonomy’ by ‘taxa::taxonomy’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::supertaxa’ by ‘taxa::supertaxa’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘metacoder::is_leaf’ by ‘taxa::is_leaf’ when loading ‘MicrobiomeAnalystR’
Warning: replacing previous import ‘igraph::diversity’ by ‘vegan::diversity’ when loading ‘MicrobiomeAnalystR’
Error: package or namespace load failed for ‘MicrobiomeAnalystR’ in namespaceExport(ns, exports):
 undefined exports: CreateFooter, CreateMDPRnwReport, CreateRHistAppendix, CreateSDPRnwReport, PreparePDFReport
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/private/var/folders/0m/3b5s367d4672dgm3snm3m2nst2fz4v/T/RtmplmZazy/Rinst99e4c8b6500/MicrobiomeAnalystR’
      -----------------------------------
ERROR: package installation failed

[agalychnica]

Hi: an update. I did the suggested:

sudo ln -sfn /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk /opt/gfortran/SDK

and it fixed the clang and SDKRoot errors, but I still get all the Warnings for all those packages as above and the namespaceExport error message. So it still fails to do the installation.

Any suggestions?

[keaton-s]

I'm having this exact issue on Linux as well

[jitsu-biome]

Also having this issue on my Windows laptop