MetaboAnalyst R instalation

[ezechm]

Please help. I try to instal Metaboanalyst R according to the tutorial : https://www.metaboanalyst.ca/MetaboAnalyst/docs/RTutorial.xhtml#1.2%20Installation
But it does not work.
Here is the reporter error:

metanr_packages()
[1] "No new packages added..."
devtools::install_github("xia-lab/MetaboAnalystR", build = TRUE, build_vignettes = FALSE)
Downloading GitHub repo xia-lab/MetaboAnalystR@HEAD
Skipping 9 packages not available: Biobase, pcaMethods, siggenes, MSnbase, impute, fgsea, edgeR, BiocParallel, RBGL
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\ezechm\AppData\Local\Temp\RtmpEbwPgB\remotes38ec5204700\xia-lab-MetaboAnalystR-7f2fa2b/DESCRIPTION' ...
─ preparing 'MetaboAnalystR': (770ms)
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts (1s)
─ checking for empty or unneeded directories
─ building 'MetaboAnalystR_4.0.0.tar.gz'

• installing source package 'MetaboAnalystR' ...
  ** using staged installation
  ** libs
  using C++ compiler: 'G__1.EXE (GCC) 13.3.0'
  using C++11
  rm -f fortran/decorana.o c/Internal_utils_batch.o c/util.o c/fastmatch.o c/nncgc.o cpp/melt.o c/mzROI.o c/xcms_binners.o Exports.o
  gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c fortran/decorana.f -o fortran/decorana.o
  gcc -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c/Internal_utils_batch.c -o c/Internal_utils_batch.o
  c/Internal_utils_batch.c: In function 'do_decorana':
  c/Internal_utils_batch.c:114:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  114 | for (i = 0, nid = 0; i < nr*nc; i++)
  | ^~~
  c/Internal_utils_batch.c:118:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  118 | int ibegin = (int ) R_alloc(nr, sizeof(int));
  | ^~~
  gcc -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c/util.c -o c/util.o
  gcc -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c/fastmatch.c -o c/fastmatch.o
  gcc -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c/nncgc.c -o c/nncgc.o
  c/nncgc.c: In function 'objf':
  c/nncgc.c:57:11: warning: '*c[0]' may be used uninitialized [-Wmaybe-uninitialized]
  57 | return(c[0]);
  | ~~^~~~
  g++ -std=gnu++11 -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp/melt.cpp -o cpp/melt.o
  gcc -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c/mzROI.c -o c/mzROI.o
  gcc -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c c/xcms_binners.c -o c/xcms_binners.o
  c/xcms_binners.c:11:1: warning: "/" within comment [-Wcomment]
  11 | /
  |
  c/xcms_binners.c: In function '_breaks_on_binSize':
  c/xcms_binners.c:361:7: warning: unused variable 'idx' [-Wunused-variable]
  361 | int idx = 0;
  | ^~~
  g++ -std=gnu++11 -I"C:/Users/ezechm/AppData/Local/Programs/R/R-441.2/include" -DNDEBUG -I'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/Rcpp/include' -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Exports.cpp -o Exports.o
  g++ -shared -s -static-libgcc -o MetaboAnalystR.dll tmp.def fortran/decorana.o c/Internal_utils_batch.o c/util.o c/fastmatch.o c/nncgc.o cpp/melt.o c/mzROI.o c/xcms_binners.o Exports.o -fopenmp -LC:/Users/ezechm/AppData/Local/Programs/R/R-441.2/bin/x64 -lRlapack -LC:/Users/ezechm/AppData/Local/Programs/R/R-441.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/lib -LC:/Users/ezechm/AppData/Local/Programs/R/R-441.2/bin/x64 -lR
  installing to C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/00LOCK-MetaboAnalystR/00new/MetaboAnalystR/libs/x64
  ** R
  ** 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
  Error: package or namespace load failed for 'MetaboAnalystR' in namespaceExport(ns, exports):
  undefined exports: Plot.sampletrend, plot_dist
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing 'C:/Users/ezechm/AppData/Local/Programs/R/R-4.4.2/library/MetaboAnalystR'
  Warning message:
  In i.p(...) :
  installation of package ‘C:/Users/ezechm/AppData/Local/Temp/RtmpEbwPgB/file38ec43f53b47/MetaboAnalystR_4.0.0.tar.gz’ had non-zero exit status

[AlexHoratio]

I have the same problem.

It looks like those two functions are actually called Plot.sample.trend and Plot.sample.dist in R/batch_effect_utils.r (unlike what they are called in NAMESPACE) , maybe this is the source of the issue?

[xukainju]

I have the same problem.

It looks like those two functions are actually called Plot.sample.trend and Plot.sample.dist in R/batch_effect_utils.r (unlike what they are called in NAMESPACE) , maybe this is the source of the issue?

Correlating the Plot.sample.dist with plot.sample.dist, Plot.sample.trend with plot.sample.trend in the NAMESAPCE file will solve the problem. Many thanks!

[Ganodermataceae69]

I installed all the dependencies manually and then installed MetaboAnalystR using the devtools code without issues. The dependencies are not anymore on CRAN repository, so you have to use bioconductor repository to download them using BiocManager (p.e. BiocManager::install("KEGGgraph"))

[ezechm]

I installed all the dependencies manually and then installed MetaboAnalystR using the devtools code without issues. The dependencies are not anymore on CRAN repository, so you have to use bioconductor repository to download them using BiocManager (p.e. BiocManager::install("KEGGgraph"))

I try this and installed dependencies by BiocManager but the problem remains. I still have the same issue with the Metaboanalyst R instalation.

[Ganodermataceae69]

That's because there are extra dependencies not listed in the code provided in the tutorial. Download the MetaboAnalystR tar.gz file and try to install it using the file. It will tell you that you need to install more dependencies. However I haven't been able to perform my analysis as I got an error in the first step (ROI extraction) despite I was able to install the 3.3 version using the .tar.gz file

[JenMcCavitt]

I am also having the same problem as ezechm and AlexHoratio (Windows 11, R version 4.5.0). I have tried all three install options on the MetaboAnalyst website which generated the same error. I also tried:

devtools::install_github("https://github.com/mvaniterson/SSPA")

In case there was problem with SSPA being depreciated. No luck here either.

It seems as if @xukainju is correct and that the issue lies with the NAMESPACE file, but I am unsure how to fix this. Has anyone come across a solution? MetaboAnalystR was working perfectly for me this time last year, but I unfortunately did not make a note of the R version and package versions at the time.

Apologies if I am missing necessary information for troubleshooting, I am new to R and easily confused.

[ivangong24]

Hi all, I encountered this issue as well. Yes, @xukainju is correct and that the issue lies with the NAMESPACE file. Here is how I solve it: I first downloaded the source code from github using git clone https://github.com/xia-lab/MetaboAnalystR.git, then I modified the NAMESPACE file by replacing the function names with AlexHoratio suggested. Then open cmd and type in R CMD build C:\Users\username\MetaboAnalystR and R CMD INSTALL C:\Users\username\MetaboAnalystR_4.0.0.tar.gz. The installation will work if you have all the dependencies installed.

[jchmiel4]

Had the same issue and was able to install via PR #350

devtools::install_github("xia-lab/MetaboAnalystR@refs/pull/350/head", build = TRUE, build_vignettes = TRUE, build_manual =T)

[JenMcCavitt]

Had the same issue and was able to install via PR #350

devtools::install_github("xia-lab/MetaboAnalystR@refs/pull/350/head", build = TRUE, build_vignettes = TRUE, build_manual =T)

Thank you @jchmiel4 - this worked for me! I then ran into issue #349 but the solution there fixed it.

[eroell]

Hey, @jchmiel4's approach worked for me, but it would be really helpful to fix this, such that users don't need to rely on a comment in an issue, that fetches from a Pull Request. To my understanding, every install of metaboanalyst with the devtools approach is failing right now?