[ Started: 2023-09-06 02:35:11 CEST ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-devel/lib/R/library" Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21) Old packages: 'spatstat.geom' trying URL 'https://cloud.r-project.org/src/contrib/spatstat.geom_3.2-5.tar.gz' Content type 'application/x-gzip' length 771489 bytes (753 KB) ================================================== downloaded 753 KB * installing *source* package ‘spatstat.geom’ ... ** package ‘spatstat.geom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c areadiff.c -o areadiff.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c auctionbf.c -o auctionbf.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bdrymask.c -o bdrymask.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c close3pair.c -o close3pair.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c closepair.c -o closepair.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c connectgraph.c -o connectgraph.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c connectpix.c -o connectpix.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dinfty.c -o dinfty.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c discarea.c -o discarea.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c discs.c -o discs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dist2dpath.c -o dist2dpath.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c distan3.c -o distan3.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c distances.c -o distances.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c distmapbin.c -o distmapbin.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dwpure.c -o dwpure.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c exactPdist.c -o exactPdist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c exactdist.c -o exactdist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fardist.c -o fardist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hasclose.c -o hasclose.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hotrod.c -o hotrod.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c knndistance.c -o knndistance.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c knngrid.c -o knngrid.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c loccum.c -o loccum.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c metricPdist.c -o metricPdist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minnnd.c -o minnnd.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nearestpix.c -o nearestpix.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nn3Ddist.c -o nn3Ddist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nnMDdist.c -o nnMDdist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nndistance.c -o nndistance.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nngrid.c -o nngrid.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c periodic.c -o periodic.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c poly2im.c -o poly2im.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c quasirandom.c -o quasirandom.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raster.c -o raster.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rasterfilter.c -o rasterfilter.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scan.c -o scan.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c seg2pix.c -o seg2pix.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabnum.c -o tabnum.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c trigraf.c -o trigraf.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c uniquemap.c -o uniquemap.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c veegraf.c -o veegraf.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c whist.c -o whist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c xyseg.c -o xyseg.o gcc -shared -L/usr/local/lib -o spatstat.geom.so areadiff.o auctionbf.o bdrymask.o close3pair.o closepair.o connectgraph.o connectpix.o dinfty.o discarea.o discs.o dist2dpath.o distan3.o distances.o distmapbin.o dwpure.o exactPdist.o exactdist.o fardist.o hasclose.o hotrod.o init.o knndistance.o knngrid.o loccum.o metricPdist.o minnnd.o nearestpix.o nn3Ddist.o nnMDdist.o nndistance.o nngrid.o periodic.o poly2im.o quasirandom.o raster.o rasterfilter.o scan.o seg2pix.o tabnum.o trigraf.o uniquemap.o veegraf.o whist.o xyseg.o installing to /home/omnipath/local/R/4.3-3.17/00LOCK-spatstat.geom/00new/spatstat.geom/libs ** R ** inst ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spatstat.geom) The downloaded source packages are in ‘/tmp/RtmpuqdAH8/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2023-09-06 02:35:46 CEST ]