starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to 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environment variable `R_LIBS_SITE' set to `/gnu/store/h0n8f70hqc3xlyvnwadp1xw3gixcsbz6-r-lattice-0.20-45/site-library/' environment variable `CPATH' set to `/gnu/store/hga7z27qxs55qjwkfda1q20wsfw20xls-gfortran-10.3.0/include:/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/include:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/include:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/include:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/include:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/include:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/include:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/include:/gnu/store/wsx4kz1gh6cpdhx393frhqknmswbggq8-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to 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`/gnu/store/hga7z27qxs55qjwkfda1q20wsfw20xls-gfortran-10.3.0/include:/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/include:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/include:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/include:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/include:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/include:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/include:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/include:/gnu/store/wsx4kz1gh6cpdhx393frhqknmswbggq8-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to 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'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' nlme/ nlme/NAMESPACE nlme/LICENSE.note nlme/ChangeLog nlme/data/ nlme/data/Muscle.rda nlme/data/Dialyzer.rda nlme/data/MathAchieve.rda nlme/data/Phenobarb.rda nlme/data/Relaxin.rda nlme/data/Orthodont.rda nlme/data/IGF.rda nlme/data/Tetracycline1.rda nlme/data/Earthquake.rda nlme/data/PBG.rda nlme/data/Alfalfa.rda nlme/data/Quinidine.rda nlme/data/Fatigue.rda nlme/data/Oxide.rda nlme/data/Wafer.rda nlme/data/Pixel.rda nlme/data/bdf.rda nlme/data/Remifentanil.rda nlme/data/Oxboys.rda nlme/data/RatPupWeight.rda nlme/data/Gasoline.rda nlme/data/ergoStool.rda nlme/data/BodyWeight.rda nlme/data/Nitrendipene.rda nlme/data/Glucose2.rda nlme/data/Wheat.rda nlme/data/Cefamandole.rda nlme/data/Ovary.rda nlme/data/Gun.rda nlme/data/Oats.rda nlme/data/Assay.rda nlme/data/Tetracycline2.rda nlme/data/MathAchSchool.rda nlme/data/Meat.rda nlme/data/Milk.rda nlme/data/Machines.rda 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nlme/man/getCovariate.corStruct.Rd nlme/man/Variogram.corSpher.Rd nlme/man/predict.lme.Rd nlme/man/gnlsControl.Rd nlme/man/fixed.effects.Rd nlme/man/Oxboys.Rd nlme/man/Names.pdMat.Rd nlme/man/pdFactor.reStruct.Rd nlme/TODO nlme/DESCRIPTION nlme/build/ nlme/build/partial.rdb nlme/tests/ nlme/tests/anova.gls.R nlme/tests/extras.Rin nlme/tests/deviance.R nlme/tests/lme.R nlme/tests/updateLme.R nlme/tests/scoping.R nlme/tests/deparse.R nlme/tests/coef.Rout.save nlme/tests/nlme2.R nlme/tests/gnls-ch8.R nlme/tests/data.frame.R nlme/tests/nlme.R nlme/tests/missing.R nlme/tests/lme.Rout.save nlme/tests/augPredmissing.R nlme/tests/predict.lme.R nlme/tests/gls.R nlme/tests/getVarCov.R nlme/tests/getData.R nlme/tests/varIdent.R nlme/tests/extras/ nlme/tests/extras/README nlme/tests/extras/mlbook.Rout.save nlme/tests/extras/scripts.R nlme/tests/extras/scripts.Rout.save nlme/tests/extras/mlbook.R nlme/tests/extras/nlme-stall.R nlme/tests/missing.Rout.save nlme/tests/ss2.rds nlme/tests/contrMat.R nlme/tests/sigma-fixed-etc.R nlme/tests/lmList.R nlme/tests/varConstProp.R nlme/tests/fitted.R nlme/tests/coef.R nlme/tests/corFactor.R nlme/tests/augPred_lab.R nlme/src/ nlme/src/nlmefit.c nlme/src/matrix.h nlme/src/nlmefit.h nlme/src/pdMat.h nlme/src/init.c nlme/src/pdMat.c nlme/src/gnls.c nlme/src/Makevars nlme/src/rs.f nlme/src/pythag.c nlme/src/matrix.c nlme/src/chol.f nlme/src/nlme.c nlme/src/base.h nlme/src/corStruct.c nlme/src/nlOptimizer.c nlme/src/nlOptimizer.h nlme/R/ nlme/R/newMethods.R nlme/R/lme.R nlme/R/newGenerics.R nlme/R/VarCorr.R nlme/R/VarCov.R nlme/R/simulate.R nlme/R/nlme.R nlme/R/gls.R nlme/R/modelStruct.R nlme/R/reStruct.R nlme/R/pdMat.R nlme/R/zzMethods.R nlme/R/varFunc.R nlme/R/nlsList.R nlme/R/gnls.R nlme/R/lmList.R nlme/R/newFunc.R nlme/R/corStruct.R nlme/R/groupedData.R nlme/MD5 nlme/inst/ nlme/inst/CITATION nlme/inst/mlbook/ nlme/inst/mlbook/README nlme/inst/mlbook/ch04.R nlme/inst/mlbook/ch05.R nlme/inst/po/ nlme/inst/po/ko/ nlme/inst/po/ko/LC_MESSAGES/ nlme/inst/po/ko/LC_MESSAGES/R-nlme.mo nlme/inst/po/ko/LC_MESSAGES/nlme.mo nlme/inst/po/fr/ nlme/inst/po/fr/LC_MESSAGES/ nlme/inst/po/fr/LC_MESSAGES/R-nlme.mo nlme/inst/po/fr/LC_MESSAGES/nlme.mo nlme/inst/po/de/ nlme/inst/po/de/LC_MESSAGES/ nlme/inst/po/de/LC_MESSAGES/R-nlme.mo nlme/inst/po/de/LC_MESSAGES/nlme.mo nlme/inst/po/pl/ nlme/inst/po/pl/LC_MESSAGES/ nlme/inst/po/pl/LC_MESSAGES/R-nlme.mo nlme/inst/po/pl/LC_MESSAGES/nlme.mo nlme/inst/po/en@quot/ nlme/inst/po/en@quot/LC_MESSAGES/ nlme/inst/po/en@quot/LC_MESSAGES/R-nlme.mo nlme/inst/po/en@quot/LC_MESSAGES/nlme.mo nlme/inst/scripts/ nlme/inst/scripts/ch03.R nlme/inst/scripts/ch01.R nlme/inst/scripts/runme.R nlme/inst/scripts/ch04.R nlme/inst/scripts/ch05.R nlme/inst/scripts/ch08.R nlme/inst/scripts/ch06.R nlme/inst/scripts/ch02.R nlme/inst/scripts/sims.rda nlme/po/ nlme/po/R-nlme.pot nlme/po/nlme.pot nlme/po/R-ko.po nlme/po/pl.po nlme/po/ko.po nlme/po/R-pl.po nlme/po/R-de.po nlme/po/R-fr.po nlme/po/de.po nlme/po/fr.po phase `unpack' succeeded after 0.2 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory * installing *source* package ‘nlme’ ... ** package ‘nlme’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gfortran -fno-optimize-sibling-calls -fpic -g -O2 -c chol.f -o chol.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c corStruct.c -o corStruct.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c gnls.c -o gnls.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c matrix.c -o matrix.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c nlOptimizer.c -o nlOptimizer.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c nlme.c -o nlme.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c nlmefit.c -o nlmefit.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c pdMat.c -o pdMat.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c pythag.c -o pythag.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -c rs.f -o rs.o gcc -shared -L/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/lib -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L/gnu/store/qcli7b46b2v31kg7arbinqphx1srzqhd-gfortran-10.3.0-lib/lib/gcc/i686-unknown-linux-gnu/10.3.0 -L/gnu/store/qcli7b46b2v31kg7arbinqphx1srzqhd-gfortran-10.3.0-lib/lib -lgfortran -lm -lquadmath -L/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/lib -lR installing to /gnu/store/agcawlxb42f2qp141ydmshnv1vivvxnm-r-nlme-3.1-158/site-library/00LOCK-nlme/00new/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** tests ** byte-compile and prepare package for lazy loading Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** help *** installing help indices ** building package indices Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** testing if installed package can be loaded from temporary location Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** testing if installed package keeps a record of temporary installation path * DONE (nlme) phase `install' succeeded after 60.6 seconds starting phase `check' Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Testing examples for package ‘nlme’ phase `check' succeeded after 107.0 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `make-dynamic-linker-cache' phase `make-dynamic-linker-cache' succeeded after 0.0 seconds starting phase `install-license-files' installing 1 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds