MicrobiomeAnalystR failed to install - namespaceExport(ns, exports)

[mlosada323]

Hi there,

I've tried to install MicrobiomeAnalystR using devtools and Cloning Github and install locally, and both options gave me the same error below. The full output is further below. Does anybody know a way around?

Best

Marcos

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

######## full error via devtools

devtools::install_github("xia-lab/MicrobiomeAnalystR", build = T)
Downloading GitHub repo xia-lab/MicrobiomeAnalystR@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: curl (6.0.0 -> 6.0.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/5k/2q0sf5bx5gx6x350py4pmpzr0000gq/T/RtmpSHFU23/remotes17c5f124e973/xia-lab-MicrobiomeAnalystR-b958ea1/DESCRIPTION’ ...
─ preparing ‘MicrobiomeAnalystR’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ excluding invalid files
Subdirectory 'R' contains invalid file names:
‘rscripts’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘MicrobiomeAnalystR_2.0.tar.gz’

• installing source package ‘MicrobiomeAnalystR’ ...
  ** using staged installation
  ** libs
  using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.4)’
  sh: usr/local/gfortran/bin/gfortran: No such file or directory
  using SDK: ‘MacOSX15.1.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/usr/local/gfortran/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/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 ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MicrobiomeAnalystR’
  Warning messages:
  1: In readLines(old_path) :
  incomplete final line found on '/Users/mlosada/.R/Makevars'
  2: In i.p(...) :
  installation of package ‘/var/folders/5k/2q0sf5bx5gx6x350py4pmpzr0000gq/T//RtmpSHFU23/file17c5f1e5a7d9b/MicrobiomeAnalystR_2.0.tar.gz’ had non-zero exit status

######## full error via Clone Github and install locally

mlosada@GW-NCC77VJ Desktop % 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 16.0.0 (clang-1600.0.26.4)’
  sh: usr/local/gfortran/bin/gfortran: No such file or directory
  using SDK: ‘MacOSX15.1.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/usr/local/gfortran/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  installing to /private/var/folders/5k/2q0sf5bx5gx6x350py4pmpzr0000gq/T/RtmpdwfI6W/Rinste85987ecd9/00LOCK-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/5k/2q0sf5bx5gx6x350py4pmpzr0000gq/T/RtmpdwfI6W/Rinste85987ecd9/MicrobiomeAnalystR’
  -----------------------------------
  ERROR: package installation failed
  mlosada@GW-NCC77VJ Desktop %

[gkuhlenbaum]

Hello Marcos,

I have exactly the same issue and can't find a workaround.....
Help would be much appreciated.

Yours sincerely

Gregor

[Aciole-David]

@mlosada323 and @gkuhlenbaum,

How you doing?
Sorry but I think you guys should read the many previous issues related to install, which are all pretty similar, and also consider that the package remains "not finished", while those errors are not well documented officially by Xia-lab folks (not me)

I'd like to help with my experience on that, but, as expected when troubleshooting, it'd be nice if you better described in order to reproduce the errors: SO, R, rstudio? dependencies check? ect...

Best wishes,
David

[diego-iac]

Hi, same error here and same as agalychnica in the previous issues. After some warnings, the installation process stops saying:

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

SO: Ubuntu 22.04.4 LTS 64bit
R.version :
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 4.1
year 2024
month 06
day 14
svn rev 86737
language R
version.string R version 4.4.1 (2024-06-14)
nickname Race for Your Life

[abf-code]

Hi! I was getting the same errors. After some work I was able to make the package work. I'll show you what I did (I work in Linux and I use the 4.3.3 version of R):

1) I installed packages and libraries that could be necessary to install the ones used by MicrbiomeAnalystR:

sudo apt install build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libcairo2-dev libxt-dev libfreetype6-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev pkg-config libpng-dev libtiff5-dev libjpeg-dev
sudo apt update

2) Then, I tried to install MicrobiomeAnalyst via cloning the repository and checked all the packages I had missing. I installed them in R (some are not in the CRAN repositories anymore, so I got them from GitHub):

install.packages("BiocManager")
BiocManager::install("phyloseq")
BiocManager::install("DESeq2")
BiocManager::install("genefilter")
BiocManager::install("Cairo")
BiocManager::install("edgeR")
install.packages("devtools")
install.packages("remotes")
remotes::install_github("ropensci/taxize")
remotes::install_github("kylebittinger/qiimer")
remotes::install_github("joey711/biom")
remotes::install_github("grimbough/rhdf5")
remotes::install_github("ropensci/bold")
devtools::install_github("grunwaldlab/metacoder")
devtools::install_github("nick-youngblut/Tax4Fun")
BiocManager::install("pryr")
BiocManager::install("viridis")
BiocManager::install("tidyverse")
BiocManager::install("limma")

3) Clone the GitHub repository

git clone https://github.com/xia-lab/MicrobiomeAnalystR.git

4) Install pandoc if you don't have it (it will be required)

sudo apt-get install pandoc

5) IMPORTANT. Go to the MicrobiomeAnalystR folder after cloning, and to the R/ folder. There you'll find a file named 'rscripts'. I renamed it to 'scripts.R'. For some reason, the installation process wasn't able to recognise this file with the name provided by the authors.

6) Run:

R CMD build MicrobiomeAnalystR
R CMD INSTALL MicrobiomeAnalystR_*.tar.gz

I hope it works for you!!!

[gkuhlenbaum]

Hello Dear Sir, thanks a lot for the help which I will try. I’m not really a user but was asked to solve some problem somebody else had with the online version. However, I was able to make a little R-script which circumvented the problem… Yours sincerely Gregor Prof. Dr. med. Dr. Gregor Kuhlenbäumer Department of Neurology Kiel University Arnold-Heller Str. 3 24105 Kiel Germany 0431/500 23986 ***@***.*** Von: abf-code ***@***.*** Gesendet: Freitag, 17. Januar 2025 14:13 An: xia-lab/MicrobiomeAnalystR ***@***.***> Cc: Kuhlenbäumer, Gregor ***@***.***>; Mention ***@***.***> Betreff: Re: [xia-lab/MicrobiomeAnalystR] MicrobiomeAnalystR failed to install - namespaceExport(ns, exports) (Issue #35) Achtung, externe Mail! Hi! I was getting the same errors. After some work I was able to make the package work. I'll show you what I did (I work in Linux and I use the 4.3.3 version of R): 1) I installed packages and libraries that could be necessary to install the ones used by MicrbiomeAnalystR: sudo apt install build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libcairo2-dev libxt-dev libfreetype6-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev pkg-config libpng-dev libtiff5-dev libjpeg-dev sudo apt update 2) Then, I tried to install MicrobiomeAnalyst via cloning the repository and checked all the packages I had missing. I installed them in R (some are not in the CRAN repositories anymore, so I got them from GitHub): install.packages("BiocManager") BiocManager::install("phyloseq") BiocManager::install("DESeq2") BiocManager::install("genefilter") BiocManager::install("Cairo") BiocManager::install("edgeR") install.packages("devtools") install.packages("remotes") remotes::install_github("ropensci/taxize") remotes::install_github("kylebittinger/qiimer") remotes::install_github("joey711/biom") remotes::install_github("grimbough/rhdf5") remotes::install_github("ropensci/bold") devtools::install_github("grunwaldlab/metacoder") devtools::install_github("nick-youngblut/Tax4Fun") BiocManager::install("pryr") BiocManager::install("viridis") BiocManager::install("tidyverse") BiocManager::install("limma") 3) Clone the GitHub repository git clone https://github.com/xia-lab/MicrobiomeAnalystR.git 4) Install pandoc if you don't have it (it will be required) sudo apt-get install pandoc 5) IMPORTANT. Go to the MicrobiomeAnalystR folder after cloning, and to the R/ folder. There you'll find a file named 'rscripts'. I renamed it to 'scripts.R'. For some reason, the installation process wasn't able to recognise this file with the name provided by the authors. 6) Run: R CMD build MicrobiomeAnalystR R CMD INSTALL MicrobiomeAnalystR_*.tar.gz I hope it works for you!!! — Reply to this email directly, view it on GitHub<#35 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AQBT3Y4R3KPY5WK3DXLM5ZT2LD6U7AVCNFSM6AAAAABR5I334GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKOJYGM2DANZQGE>. You are receiving this because you were mentioned.Message ID: ***@***.***> [https://media.uksh.de/emailfooter/ukraine_202210.jpg]<https://www.uksh.de/ukrainehilfe.html> UKSH hilft Ukraine: Wir machen weiter. Helfen Sie uns, zu helfen! Unterstützung für die Menschen in und aus der Ukraine. UKSH-Gutes tun!-Spendenkonto zur Aktion Empfänger: UKSH WsG e.V. IBAN: DE75 2105 0170 1400 1352 22 | BIC: NOLADE21KIE Angabe bei Ihrer Überweisung im Verwendungszweck: FW14042: UKSH hilft Ukraine Spenden via PayPal: Spenden per PayPal<https://www.paypal.com/donate/?hosted_button_id=2ZTDYKAN8L6NY> Alle Infos: www.uksh.de/ukrainehilfe<http://www.uksh.de/ukrainehilfe> [UKSH logo] Universitätsklinikum Schleswig-Holstein Rechtsfähige Anstalt des öffentlichen Rechts der Christian-Albrechts-Universität zu Kiel und der Universität zu Lübeck Vorstandsmitglieder: Prof. Dr. Dr. h.c. mult. Jens Scholz (Vorsitzender/CEO), Peter Pansegrau (CFO), Monika Alke (COO), Prof. Dr. Thomas Münte, Prof. Dr. Joachim Thiery Vorsitzender des Aufsichtsrates: Guido Wendt Bankverbindungen: Förde Sparkasse IBAN: DE14 2105 0170 0000 1002 06 SWIFT/BIC: NOLA DE 21 KIE Commerzbank AG IBAN: DE17 2308 0040 0300 0412 00 SWIFT/BIC: DRES DE FF 230 Gemeinsam Gutes tun! Spenden: Alle UKSH-Spendenmöglichkeiten unter www.uksh.de/gutestun<http://www.uksh.de/gutestun> Spendenkonto: Förde Sparkasse IBAN: DE75 2105 0170 1400 1352 22 | BIC: NOLADE21KIE | Empfänger: UKSH WsG e.V. Diese E-Mail enthält vertrauliche Informationen und ist nur für die Personen bestimmt, an welche sie gerichtet ist. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, bitten wir Sie, uns hiervon unverzüglich zu unterrichten und die E-Mail zu vernichten. Wir weisen darauf hin, dass der Gebrauch und die Weiterleitung einer nicht bestimmungsgemäß empfangenen E-Mail und ihres Inhalts gesetzlich verboten sind und ggf. Schadensersatzansprüche auslösen können.

[Lianfuwu]

I also encountered the same issue and can't install the MicrobiomeAnalystR package on my Windows.

[diego-iac]

Hi! I was getting the same errors. After some work I was able to make the package work. I'll show you what I did (I work in Linux and I use the 4.3.3 version of R):

1) I installed packages and libraries that could be necessary to install the ones used by MicrbiomeAnalystR:

sudo apt install build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libcairo2-dev libxt-dev libfreetype6-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev pkg-config libpng-dev libtiff5-dev libjpeg-dev
sudo apt update

2) Then, I tried to install MicrobiomeAnalyst via cloning the repository and checked all the packages I had missing. I installed them in R (some are not in the CRAN repositories anymore, so I got them from GitHub):

install.packages("BiocManager")
BiocManager::install("phyloseq")
BiocManager::install("DESeq2")
BiocManager::install("genefilter")
BiocManager::install("Cairo")
BiocManager::install("edgeR")
install.packages("devtools")
install.packages("remotes")
remotes::install_github("ropensci/taxize")
remotes::install_github("kylebittinger/qiimer")
remotes::install_github("joey711/biom")
remotes::install_github("grimbough/rhdf5")
remotes::install_github("ropensci/bold")
devtools::install_github("grunwaldlab/metacoder")
devtools::install_github("nick-youngblut/Tax4Fun")
BiocManager::install("pryr")
BiocManager::install("viridis")
BiocManager::install("tidyverse")
BiocManager::install("limma")

3) Clone the GitHub repository

git clone https://github.com/xia-lab/MicrobiomeAnalystR.git

4) Install pandoc if you don't have it (it will be required)

sudo apt-get install pandoc

5) IMPORTANT. Go to the MicrobiomeAnalystR folder after cloning, and to the R/ folder. There you'll find a file named 'rscripts'. I renamed it to 'scripts.R'. For some reason, the installation process wasn't able to recognise this file with the name provided by the authors.

6) Run:

R CMD build MicrobiomeAnalystR
R CMD INSTALL MicrobiomeAnalystR_*.tar.gz

I hope it works for you!!!

Thanks a lot! I've tried only now the code you suggested but it worked just fine for me, in Ubuntu 22.04.4 LTS with R version 4.4.1

[SquillarioM]

Hi! I was getting the same errors. After some work I was able to make the package work. I'll show you what I did (I work in Linux and I use the 4.3.3 version of R):

1) I installed packages and libraries that could be necessary to install the ones used by MicrbiomeAnalystR:

sudo apt install build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libcairo2-dev libxt-dev libfreetype6-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev pkg-config libpng-dev libtiff5-dev libjpeg-dev
sudo apt update

2) Then, I tried to install MicrobiomeAnalyst via cloning the repository and checked all the packages I had missing. I installed them in R (some are not in the CRAN repositories anymore, so I got them from GitHub):

install.packages("BiocManager")
BiocManager::install("phyloseq")
BiocManager::install("DESeq2")
BiocManager::install("genefilter")
BiocManager::install("Cairo")
BiocManager::install("edgeR")
install.packages("devtools")
install.packages("remotes")
remotes::install_github("ropensci/taxize")
remotes::install_github("kylebittinger/qiimer")
remotes::install_github("joey711/biom")
remotes::install_github("grimbough/rhdf5")
remotes::install_github("ropensci/bold")
devtools::install_github("grunwaldlab/metacoder")
devtools::install_github("nick-youngblut/Tax4Fun")
BiocManager::install("pryr")
BiocManager::install("viridis")
BiocManager::install("tidyverse")
BiocManager::install("limma")

3) Clone the GitHub repository

git clone https://github.com/xia-lab/MicrobiomeAnalystR.git

4) Install pandoc if you don't have it (it will be required)

sudo apt-get install pandoc

5) IMPORTANT. Go to the MicrobiomeAnalystR folder after cloning, and to the R/ folder. There you'll find a file named 'rscripts'. I renamed it to 'scripts.R'. For some reason, the installation process wasn't able to recognise this file with the name provided by the authors.

6) Run:

R CMD build MicrobiomeAnalystR
R CMD INSTALL MicrobiomeAnalystR_*.tar.gz

I hope it works for you!!!

It worked for me too. Thanks a lot!!!