Problem installing rGEDI in R 4.2.0

fpegmbg commented 2 years ago

Thank you for the instructions about how to resolve installation issues where git or RTools are missing (https://github.com/carlos-alberto-silva/rGEDI/issues/39).

Succinct version of my problem: rGEDI installs and functions in R 4.1.3, but not in R 4.2.0.

I tried 6/21/2022 to install rGEDI with fresh installations of RTools and Git, and with R 4.2.0, using the R GUI (not R Studio), all exes downloaded same date, but the installation fails in 4.2.0 despite working in 4.1.3.

Confirming I am using RTools 4.0, and git from below link.

Sys.which("make") make "C:\rtools40\usr\bin\make.exe" Git from https://git-scm.com/ (win 64 bit version)

I updated devtools, getPass, and hdf5r but the devtools installation fails in R 4.2.0. If however I install in R 4.1.3 (from March 2022), with otherwise no change to git or Rtools, I can complete the installation with no errors and just one warning (could not update package "BH").

The installation output when it fails in 4.2.0 is: Downloading git repo https://github.com/carlos-alberto-silva/rGEDI "C:\PROGRA~1\Git\cmd\git.exe" clone --depth 1 --no-hardlinks https://github.com/carlos-alberto-silva/rGEDI C:\Users...\AppData\Local\Temp\RtmpOeS17I\file1a584eb3d04 "C:\PROGRA~1\Git\cmd\git.exe" clone --depth 1 --no-hardlinks --recurse-submodules https://github.com/caiohamamura/libclidar C:\Users...\AppData\Local\Temp\RtmpOeS17I\file1a584eb3d04/src/libclidar "C:\PROGRA~1\Git\cmd\git.exe" clone --depth 1 --no-hardlinks --recurse-submodules https://github.com/caiohamamura/tools C:\Users...\AppData\Local\Temp\RtmpOeS17I\file1a584eb3d04/src/tools "C:\PROGRA~1\Git\cmd\git.exe" clone --depth 1 --no-hardlinks --recurse-submodules https://bitbucket.org/caiohamamura/gedisimulator C:\Users...\AppData\Local\Temp\RtmpOeS17I\file1a584eb3d04/src/gedisimulator

checking for file 'C:\Users...\AppData\Local\Temp\RtmpOeS17I\file1a584eb3d04/DESCRIPTION' ...

✔ checking for file 'C:\Users...\AppData\Local\Temp\RtmpOeS17I\file1a584eb3d04/DESCRIPTION'

─ preparing 'rGEDI': (1.5s) checking DESCRIPTION meta-information ...

checking DESCRIPTION meta-information ...

✔ checking DESCRIPTION meta-information ─ cleaning src

─ checking for LF line-endings in source and make files and shell scripts (349ms)

─ checking for empty or unneeded directories

Omitted 'LazyData' from DESCRIPTION

─ building 'rGEDI_0.3.0.tar.gz'

Warning:

Warning: file 'rGEDI/cleanup' did not have execute permissions: corrected

Warning: file 'rGEDI/configure' did not have execute permissions: corrected

Warning:

Warning: file 'rGEDI/src/gedisimulator/configure' did not have execute permissions: corrected

installing source package 'rGEDI' ... ** using staged installation

WARNING: this package has a configure script It probably needs manual configuration

** libs "C:/PROGRA~1/R/R-42~1.0/bin/Rscript" "../tools/winlibs.R" 1.8.16 [1] "Downloading and unpacking GSL..." [1] "Downloading and unpacking HDF5..." "C:/PROGRA~1/R/R-42~1.0/bin/Rscript" "../tools/deps.R" gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c libclidar/libLasProcess.c -o libclidar/libLasProcess.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c libclidar/libLasRead.c -o libclidar/libLasRead.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c libclidar/gaussFit.c -o libclidar/gaussFit.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c libclidar/libLidVoxel.c -o libclidar/libLidVoxel.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c libclidar/libTLSread.c -o libclidar/libTLSread.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c libclidar/libLidarHDF.c -o libclidar/libLidarHDF.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gedisimulator/gediIO.c -o gedisimulator/gediIO.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -Igedisimulator -Itools -Icmpfit-1.2 -Ilibclidar -I. -I../windows/hdf5-1.8.16/include -I../windows/gsl-2.4/include -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -DDLLEXPORT -D_USE_MATH_DEFINES -D_WIN32 -DWIN32 -DH5_BUILT_AS_DYNAMIC_LIB -DDLL_EXPORTS -DUSEPHOTON -DWITHOUT_GDAL -DUSE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gedisimulator/photonCount.c -o gedisimulator/photonCount.o gedisimulator/photonCount.c: In function 'pickArrayElement':

... more similar to this, ending with:

C:/rtools40/ucrt64/bin/../lib/gcc/x86_64-w64-mingw32/10.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/hdf5-1.8.16/lib-4.9.3/x64/libhdf5.a(H5Eint.c.obj):H5Eint.c:(.text+0x224): more undefined references to `__imp___iob_func' follow collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'rGEDI'

removing 'C:/Program Files/R/R-4.2.0/library/rGEDI' Warning message: In i.p(...) : installation of package ‘C:/Users/.../rGEDI_0.3.0.tar.gz’ had non-zero exit status

caiohamamura commented 2 years ago

3de17a087ed15d12a8e91082a47dff5ecda66411 should fix it! Please, try again!

fpegmbg commented 2 years ago

Hi Caio, thank you very much for fixing the package to run in 4.2! I appreciate your time, and thanks for making this avaialable to everyone! Thanks, Tom

From: Caio Hamamura @.> Sent: Tuesday, July 5, 2022 9:47 AM To: carlos-alberto-silva/rGEDI @.> Cc: Tom Baribault @.>; Author @.> Subject: Re: [carlos-alberto-silva/rGEDI] Problem installing rGEDI in R 4.2.0 (Issue #40)

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carlos-alberto-silva / rGEDI

Problem installing rGEDI in R 4.2.0 #40