gitter for R 4.0.2? about gitter HOT 5 CLOSED

Does it not work as expected now?

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from gitter.

Since gitter as well as its dependency PET are now removed from CRAN I installed the packages using:

devtools::install_github("cran/PET")
devtools::install_github("omarwagih/gitter")

Unfortunately, PET can't be compiled with gcc>9 because a multiple variable definition error in this package will not be ignored anymore with newer C compiler versions. I was able to install the package after using a ~/.R/Makevars file with content CC=gcc-9 or adding -fcommon to variable CFLAGS.

from gitter.

Hi,
I have a similar problem when I install PET. Do you know how can we solve this?
Thanks so much
** libs gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Hough.c -o Hough.o Hough.c: In function 'Hough4': Hough.c:41:10: warning: variable 'theta_min' set but not used [-Wunused-but-set-variable] 41 | double theta_min; | ^~~~~~~~~ Hough.c:40:38: warning: variable 'y' set but not used [-Wunused-but-set-variable] 40 | double *costheta,*sintheta,theta,x,y; | ^ Hough.c: In function 'Hough3': Hough.c:118:10: warning: variable 'theta_min' set but not used [-Wunused-but-set-variable] 118 | double theta_min; | ^~~~~~~~~ Hough.c: In function 'Hough2': Hough.c:173:10: warning: variable 'theta_min' set but not used [-Wunused-but-set-variable] 173 | double theta_min; | ^~~~~~~~~ Hough.c: In function 'Hough1': Hough.c:227:10: warning: variable 'theta_min' set but not used [-Wunused-but-set-variable] 227 | double theta_min; | ^~~~~~~~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PET_init.c -o PET_init.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c amatrix.c -o amatrix.o amatrix.c: In function 'RegulateMatrix': amatrix.c:234:10: warning: variable 'tempVv' set but not used [-Wunused-but-set-variable] 234 | float *tempVv; | ^~~~~~ amatrix.c: In function 'RegulateL1Matrix': amatrix.c:289:10: warning: variable 'tempVv' set but not used [-Wunused-but-set-variable] 289 | float *tempVv; | ^~~~~~ amatrix.c: In function 'GenerateAMatrixColumn': amatrix.c:784:9: warning: variable 'onedivsq2' set but not used [-Wunused-but-set-variable] 784 | float onedivsq2,psi,pidivDeltaX,costheta,sintheta,of; | ^~~~~~~~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c art.c -o art.o art.c: In function 'FAST_ART': art.c:128:10: warning: variable 'tempXv' set but not used [-Wunused-but-set-variable] 128 | float *tempXv,*tempBv; | ^~~~~~ art.c: In function 'SLOW_ART': art.c:239:10: warning: variable 'tempXv' set but not used [-Wunused-but-set-variable] 239 | float *tempXv,*tempBv; | ^~~~~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc.c -o calc.o calc.c: In function 'BackFilter': calc.c:335:19: warning: variable 'M' set but not used [-Wunused-but-set-variable] 335 | int i,m,n,mm,nn,M,N,OldHeight,OldWidth; | ^ calc.c: In function 'CentralSliceCZ': calc.c:700:49: warning: variable 'rhomin' set but not used [-Wunused-but-set-variable] 700 | float DC,deltatheta,theta,thetaadj,*realtheta,rhomin,deltarho; | ^~~~~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cg.c -o cg.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c em.c -o em.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c eval.c -o eval.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c imgtools.c -o imgtools.o imgtools.c: In function 'ReadPET': imgtools.c:1005:10: warning: variable 'result' set but not used [-Wunused-but-set-variable] 1005 | size_t result; | ^~~~~~ imgtools.c: In function 'ReadFIFHeader': imgtools.c:1148:10: warning: variable 'result' set but not used [-Wunused-but-set-variable] 1148 | size_t result; | ^~~~~~ imgtools.c: In function 'ReadFIF': imgtools.c:1222:10: warning: variable 'result' set but not used [-Wunused-but-set-variable] 1222 | size_t result; | ^~~~~~ imgtools.c: In function 'ReadAnalyze': imgtools.c:1616:10: warning: variable 'result' set but not used [-Wunused-but-set-variable] 1616 | size_t result; | ^~~~~~ imgtools.c:1614:21: warning: variable 'OffSet' set but not used [-Wunused-but-set-variable] 1614 | float ScaleFactor,OffSet; | ^~~~~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iradon.c -o iradon.o iradon.c: In function 'iradon': iradon.c:271:5: warning: 'spectrum' may be used uninitialized in this function [-Wmaybe-uninitialized] 271 | FreeImage(spectrum); | ^~~~~~~~~~~~~~~~~~~ iradon.c: In function 'loadFile': iradon.c:568:9: warning: 'list' may be used uninitialized in this function [-Wmaybe-uninitialized] 568 | return(list); | ^ iradon.c:404:16: warning: 'typeF' may be used uninitialized in this function [-Wmaybe-uninitialized] 404 | OutImage = ReadImage(fileName, typeF); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ iradon.c: In function 'writeFile': iradon.c:684:19: warning: 'N' may be used uninitialized in this function [-Wmaybe-uninitialized] 684 | SaveImage=NewFloatImage(fileName, M, N, _RealArray); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iradon.c:684:19: warning: 'M' may be used uninitialized in this function [-Wmaybe-uninitialized] iradon.c:772:5: warning: 'typeF' may be used uninitialized in this function [-Wmaybe-uninitialized] 772 | WriteImage(SaveImage, typeF); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c it.c -o it.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c itreadargs.c -o itreadargs.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c misc.c -o misc.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c oradLI.c -o oradLI.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c oradNN.c -o oradNN.o gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c oradSINC.c -o oradSINC.o oradSINC.c: In function 'radonSINC': oradSINC.c:52:10: warning: variable 'idx' set but not used [-Wunused-but-set-variable] 52 | double idx,mintrig,psi; | ^~~ gcc -I"C:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse.c -o sparse.o sparse.c: In function 'ReadSIFHeader': sparse.c:607:10: warning: variable 'result' set but not used [-Wunused-but-set-variable] 607 | size_t result; | ^~~~~~ sparse.c: In function 'ReadSIF': sparse.c:657:10: warning: variable 'result' set but not used [-Wunused-but-set-variable] 657 | size_t result; | ^~~~~~ sparse.c: In function 'MeanFilterVector': sparse.c:1537:13: warning: variable 'area' set but not used [-Wunused-but-set-variable] 1537 | float sum,area,*tempVv,*tempNv,*tempKernM; | ^~~~ gcc -shared -s -static-libgcc -o PET.dll tmp.def Hough.o PET_init.o amatrix.o art.o calc.o cg.o em.o eval.o imgtools.o iradon.o it.o itreadargs.o misc.o oradLI.o oradNN.o oradSINC.o sparse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-42~1.0/bin/x64 -lR C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: it.o:it.c:(.bss+0x610): multiple definition of DebugNiveau'; iradon.o:iradon.c:(.data+0x0): first defined here
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: it.o:it.c:(.bss+0x480): multiple definition of IniFile'; iradon.o:iradon.c:(.bss+0x0): first defined here C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: it.o:it.c:(.bss+0x598): multiple definition of multtemp'; iradon.o:iradon.c:(.bss+0x118): first defined here
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: it.o:it.c:(.bss+0x5a0): multiple definition of LogFileName'; iradon.o:iradon.c:(.bss+0x120): first defined here C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: it.o:it.c:(.bss+0x608): multiple definition of LogFile'; iradon.o:iradon.c:(.bss+0x188): first defined here
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'PET'

• removing 'C:/Users/Trinh/AppData/Local/R/win-library/4.2/PET'
  Warning message:
  In i.p(...) :
  installation of package ‘C:/Users/Trinh/AppData/Local/Temp/RtmpWSM8Xg/file6b20734d3180/PET_0.5.1.tar.gz’ had non-zero exit status
  `

from gitter.

PET has been causing a lot of issues and is no longer being actively maintained in CRAN. gitter depends on PET for radon-transformation functions (which allows you to autorotate plate images to be perfectly horizontal). I don't think many use this feature so I have removed it in the latest version of gitter (v.1.1.4) and removed the dependency on PET. Setting autorotate=TRUE will throw an error explaining the above.

This should mean that if you try install via github (using devtools::install_github), it should work smoothly now. I'll see if I can get it updated on CRAN as well.

From now on, If you want to use the autorotate feature, you'll have to figure out how to manually install PET and install an older version of gitter<=v1.1.3.

Closing this for now as it should address this issue.

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