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omarwagih / gitter

an R package for quantification of pinned microbial cultures
gitter.ccbr.utoronto.ca
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gitter for R 4.0.2? #5

Closed k-roy closed 1 year ago

omarwagih commented 4 years ago

Does it not work as expected now?

k-roy commented 4 years ago

Hi Dr. Wagih,

On R Studio I get this:

install.packages('gitter') Warning in install.packages : package ‘gitter’ is not available (for R version 4.0.2)

From the CRAN link this shows up:

Package ‘gitter’ was removed from the CRAN repository.

Formerly available versions can be obtained from the archive https://cran.r-project.org/src/contrib/Archive/gitter.

Archived on 2020-01-16 as maintainer's email address bounced and it requires archived package 'PET'.

Please use the canonical form https://CRAN.R-project.org/package=gitter https://cran.r-project.org/package=gitter to link to this page.

Kevin

Kevin R. Roy, Ph.D. Postdoctoral Scholar

Laboratory of Prof. Lars M. Steinmetz Department of Genetics Stanford University School of Medicine

Stanford Genome Technology Center

3165 Porter Drive, Room 1220 Palo Alto, CA 94304 Lab: (650) 721-5542 Cell: (310) 991-8127 kevinroy@stanford.edu kevinroy@stanford.edu

On Mon, Jun 29, 2020 at 11:03 AM Omar Wagih notifications@github.com wrote:

Does it not work as expected now?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/omarwagih/gitter/issues/5#issuecomment-651274246, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFI2EPIXXK7F36XHTAW6NKDRZDJLTANCNFSM4OKVYHYQ .

herbstk commented 2 years ago

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.

phancanhtrinh commented 1 year ago

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 ofDebugNiveau'; 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 ofmulttemp'; 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 ofLogFile'; 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'

omarwagih commented 1 year ago

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.