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 https://github.com/sqjin/CellChat/issues/5#issuecomment-1593985718, 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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/R/R-43~1.1/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:/PROGRA~1/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?