Install Package fail on windows. (file format not recognized)

[imchangchang]

Hello, I tried to install this package with R stdio on windows7, but failed with the following message:

c:\rtools40\mingw64\bin\nm.exe: CellChat_Rcpp.o: file format not recognized
......

I notice that the files under src folder are *.o and *.so, which are not windows file type. The right windows file type should be *.obj and *.dll.

Is there something wrong with my operation or this package can not install on windows?

[sqjin]

@imchangchang Hello, I have successfully installed CellChat on Windows 10. I think windows 7 might be too old. CellChat_Rcpp.o is the complied C++ code. You might need to figure out how to compile C++ code with R for Windows. This website might be helpful.

[imchangchang]

@sqjin thanks!
I just delete the *.o files and the *.so file, and reinstall CellChat. I saw the cpp files recompiled and generated a CellChat.dll file.
I think I made it :)

[sdhbiusdgb]

Hello, I tried to install this package with R studio on windows10, but failed with the following message:
ERROR: dependency 'BiocNeighbors' is not available for package 'CellChat'

[sqjin]

You should install 'BiocNeighbors' before installing cellchat

…

On Fri, Jun 16, 2023 at 10:15 AM sdhbiusdgb ***@***.***> wrote: Hello, I tried to install this package with R studio on windows10, but failed with the following message: ERROR: dependency 'BiocNeighbors' is not available for package 'CellChat' — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHXF63HMTLXH3ORTJYOD2IDXLO6TVANCNFSM4PLVBOYQ> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[Fsrgsr]

Hello，I tried to install this package with R studio on windows10，and i installed the lasted version of NMF, circlize and ComplexHeatmap. But i still can`t install CellChat successfully.
Warning message:In i.p(...) :
The value of the exit status when installing the package "C:/Users/gsrfs/AppData/Local/Temp/RtmpUVa2em/file582024621d28/CellChat_1.6.1.tar.gz" is not 0.

[Ghadeer98]

Hello, I am trying to install this package with R studio on (Windows 10), and I installed the lasted version of NMF, circlize, and ComplexHeatmap. But I am still receiving the same error message, which is:
(Error in library(CellChat, warn.conflicts = FALSE) :
there is no package called ‘CellChat’)

[sqjin]

@Ghadeer98 Have you downloaded the source codes locally and delete the *.o files and the *.so file, and reinstall CellChat.

[Ghadeer98]

I don't know exactly what you mean by locally but here (in the attached figure) is the code that I run on R studio's script

[Ghadeer98]

when I run this code (devtools::install_github("sqjin/CellChat")), i got this message (not the whole message, it is cropped):

Warning: Fortran 2018 deleted feature: Shared DO termination label 60 at (1)
g++ -std=gnu++17 -shared -s -static-libgcc -o minqa.dll tmp.def altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LC:/PROGRA1/R/R-431.1/bin/x64 -lR
installing to C:/Users/user/AppData/Local/R/win-library/4.3/00LOCK-minqa/00new/minqa/libs/x64
** R
** 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 (minqa)
• installing source package 'reticulate' ...
  ** package 'reticulate' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C++ compiler: 'G__1.EXE (GCC) 12.2.0'
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c event_loop.cpp -o event_loop.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c libpython.cpp -o libpython.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c output.cpp -o output.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c python.cpp -o python.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readline.cpp -o readline.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/user/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c signals.cpp -o signals.o
  g++ -std=gnu++17 -shared -s -static-libgcc -o reticulate.dll tmp.def RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA1/R/R-43~1.1/bin/x64 -lR
  installing to C:/Users/user/AppData/Local/R/win-library/4.3/00LOCK-reticulate/00new/reticulate/libs/x64
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  *** copying figures
  ** building package indices
  ** installing vignettes
  ** 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 (reticulate)

The downloaded source packages are in
‘C:\Users\user\AppData\Local\Temp\RtmpCMkhcl\downloaded_packages’
── R CMD build ───────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\user\AppData\Local\Temp\RtmpCMkhcl\remotes12c024231f30\sqjin-CellChat-418b660/DESCRIPTION' (613ms)
─ preparing 'CellChat': (6.2s)
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts (917ms)
─ checking for empty or unneeded directories
─ building 'CellChat_1.6.1.tar.gz'

Installing package into ‘C:/Users/user/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
ERROR: dependency 'BiocNeighbors' is not available for package 'CellChat'

• removing 'C:/Users/user/AppData/Local/R/win-library/4.3/CellChat'
  Warning messages:
  1: package ‘BiocNeighbors’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\user\AppData\Local\R\win-library\4.3\00LOCK\dplyr\libs\x64\dplyr.dll to C:\Users\user\AppData\Local\R\win-library\4.3\dplyr\libs\x64\dplyr.dll: Permission denied
3: In i.p(...) :
installation of package ‘C:/Users/user/AppData/Local/Temp/RtmpCMkhcl/file12c044e2179f/CellChat_1.6.1.tar.gz’ had non-zero exit status

[Fantasythorn]

Hello, I am trying to install this package with R studio on (Windows 10), and I installed the lasted version of NMF, circlize, and ComplexHeatmap. But I am still receiving the same error message, which is:
Error: Failed to install 'CellChat-master.zip' from local:
Could not find tools necessary to compile a package

[yeaon615]

Hello, I am trying to install this package with R studio on (Windows 10), and I installed the lasted version of NMF, circlize, and ComplexHeatmap. But I am still receiving the same error message, which is: Error: Failed to install 'CellChat-master.zip' from local: Could not find tools necessary to compile a package

Hi. Did you solve the problem？I had the same problem.

[yeaon615]

Hello, I am trying to install this package with R studio on (Windows 10), and I installed the lasted version of NMF, circlize, and ComplexHeatmap. But I am still receiving the same error message, which is: Error: Failed to install 'CellChat-master.zip' from local: Could not find tools necessary to compile a package

Hi. I have solve the similar problem by downlown the right version of Rtools according to my R version( https://cloud.r-project.org/ ). If you need the Rtools version lower than 4.2, you need to put Rtools on the PATH after installation. details: https://cloud.r-project.org/

[huatiancuoledi]

devtools::install_github("sqjin/CellChat")
Downloading GitHub repo sqjin/CellChat@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/sqjin/CellChat/tarball/HEAD' failed
how can i solve this problem?