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spatstat / spatstat.core

sub-package of spatstat containing core functionality for data analysis and modelling
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travis CV error #3

Closed jamiemkass closed 3 years ago

jamiemkass commented 3 years ago

The new spatstat.core and spatstat.geom are part of my Travis CI build, and I get this error now, which had not occurred before. Is there a fix in the works for this? Thanks very much.

* installing *source* package ‘spatstat.core’ ...

** package ‘spatstat.core’ successfully unpacked and MD5 sums checked

** using staged installation

** libs

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Ediggatsti.c -o Ediggatsti.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Ediggra.c -o Ediggra.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Efiksel.c -o Efiksel.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Egeyer.c -o Egeyer.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Estrauss.c -o Estrauss.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Kborder.c -o Kborder.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Knone.c -o Knone.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Krect.c -o Krect.o

g++ -std=gnu++11 -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Perfect.cc -o Perfect.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c areadiff.c -o areadiff.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c areaint.c -o areaint.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c areapair.c -o areapair.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c badgey.c -o badgey.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c call3d.c -o call3d.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c corrections.c -o corrections.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c denspt.c -o denspt.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c densptcross.c -o densptcross.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c dgs.c -o dgs.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c digber.c -o digber.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c diggra.c -o diggra.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c dist2.c -o dist2.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c f3.c -o f3.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c fexitc.c -o fexitc.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c fiksel.c -o fiksel.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c g3.c -o g3.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c getcif.c -o getcif.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c geyer.c -o geyer.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c hardcore.c -o hardcore.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c idw.c -o idw.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c k3.c -o k3.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c lennard.c -o lennard.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c localpcf.c -o localpcf.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c loccum.c -o loccum.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c lookup.c -o lookup.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c methas.c -o methas.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c metricPdist.c -o metricPdist.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c mhsnoop.c -o mhsnoop.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c multihard.c -o multihard.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c pcf3.c -o pcf3.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c penttinen.c -o penttinen.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c raster.c -o raster.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c rthin.c -o rthin.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c scan.c -o scan.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c segdens.c -o segdens.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c sftcr.c -o sftcr.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c sphefrac.c -o sphefrac.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c sphevol.c -o sphevol.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c straush.c -o straush.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c straushm.c -o straushm.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c strauss.c -o strauss.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c straussm.c -o straussm.o

gcc -I"/opt/R/4.0.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c triplets.c -o triplets.o

g++ -std=gnu++11 -shared -L/opt/R/4.0.2/lib/R/lib -L/usr/local/lib -o spatstat.core.so Ediggatsti.o Ediggra.o Efiksel.o Egeyer.o Estrauss.o Kborder.o Knone.o Krect.o Perfect.o areadiff.o areaint.o areapair.o badgey.o call3d.o corrections.o denspt.o densptcross.o dgs.o digber.o diggra.o dist2.o f3.o fexitc.o fiksel.o g3.o getcif.o geyer.o hardcore.o idw.o init.o k3.o lennard.o localpcf.o loccum.o lookup.o methas.o metricPdist.o mhsnoop.o multihard.o pcf3.o penttinen.o raster.o rthin.o scan.o segdens.o sftcr.o sphefrac.o sphevol.o straush.o straushm.o strauss.o straussm.o triplets.o -L/opt/R/4.0.2/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-spatstat.core/00new/spatstat.core/libs

** R

** inst

** byte-compile and prepare package for lazy loading

Error: package or namespace load failed for ‘spatstat.geom’:

 (converted from warning) replacing previous import ‘spatstat.utils::RelevantNA’ by ‘spatstat.sparse::RelevantNA’ when loading ‘spatstat.geom’

Error: package ‘spatstat.geom’ could not be loaded

Execution halted

ERROR: lazy loading failed for package ‘spatstat.core’

* removing ‘/usr/local/lib/R/site-library/spatstat.core’

Error in i.p(...) : 

  (converted from warning) installation of package ‘spatstat.core’ had non-zero exit status

Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p

Execution halted

The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .
baddstats commented 3 years ago

This is a temporary problem caused by the upgrade sequence. We have moved a few functions from spatstat.sparse to spatstat.utils. You are currently running spatstat.utils 2.x and spatstat.sparse 1.x which causes a warning about duplicated functions. If you update spatstat.sparse to version 2.0 this duplication will disappear.

baddstats commented 3 years ago

The output indicates that you have an old version of 'spatstat' hanging around. I suggest you uninstall spatstat, or re-install the new spatstat 2.0.x from CRAN.

spatstat.sparse 2.0 has been submitted to CRAN so you will be able to install it from CRAN in a day or two.

Prof Adrian Baddeley HonDSc FAA

John Curtin Distinguished Professor

School of Electrical Engineering, Computing and Mathematical Sciences

Curtin University, Perth, Western Australia

I work Mondays, Wednesdays and Thursdays only

From: Jamie M. Kass @.> Sent: Tuesday, 16 March 2021 11:59 AM To: spatstat/spatstat.core @.> Cc: Adrian Baddeley @.>; Comment @.> Subject: Re: [spatstat/spatstat.core] travis CV error (#3)

Thanks for the quick reply. When I try to install spatstat.sparse from the Github repo, I get this error.

devtools::install_github("spatstat/spatstat.sparse") Registered S3 method overwritten by 'cli': method from print.boxx spatstat Downloading GitHub repo spatstat/spatstat.sparse@HEAD Error: Failed to install 'spatstat.sparse' from GitHub: lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/withr/R/withr.rdb' is corrupt In addition: Warning message: In get0(oNam, envir = ns) : internal error -3 in R_decompress1

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jamiemkass commented 3 years ago

Great, thanks Adrian. Just for the record, and in case anyone else has this issue before the new version gets to CRAN, adding this to the Travis .yml fixes the error:

r_github_packages:
  - spatstat/spatstat.sparse