>>>>> Jarrod Hadfield <j.hadfi...@ed.ac.uk> >>>>> on Tue, 27 Jul 2010 21:37:09 +0100 writes:
> Hi, I ran R (version 2.9.0) CMD build under root in > Fedora (9). When it tried to remove "junk files" it > removed EVERYTHING in my local account! (See below). > Can anyone tell me what happened, the culprit may lay here: >> * removing junk files >> unlink MCMCglmm_2.05/R/ residuals.MCMCglmm.R >> ~ where it seems that someone (you?) have added a newline in the filname, so instead of 'residuals.MCMCglmm.R~' you got 'residuals.MCMCglmm.R ~' and the unlink / rm command interpreted '~' as your home directory. But I can hardly believe it. This seems explanation seems a bit doubtful to me.. ... > and even more importantly if I can I restore what was lost. well, you just get it from the backup. You do daily backups, do you? Regards, Martin Maechler, ETH Zurich > Panickingly, > Jarrod > [jar...@localhost AManal]$ R CMD build MCMCglmm_2.05 > * checking for file 'MCMCglmm_2.05/DESCRIPTION' ... OK > * preparing 'MCMCglmm_2.05': > * checking DESCRIPTION meta-information ... OK > * cleaning src > * installing the package to re-build vignettes > * Installing *source* package ?MCMCglmm? ... > ** libs > g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c MCMCglmm.cc -o > MCMCglmm.o > MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*, > int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, > int*, int*, double*, double*, int*, int*, int*, int*, int*, int*, > int*, int*, int*, int*, double*, double*, double*, int*, int*, int*, > int*, double*, double*, double*, int*, double*, bool*, double*, > double*, int*, int*, int*, int*, int*, double*, int*, int*, int*, > double*, double*, double*, int*, int*, double*, int*, int*, int*, > int*, double*, double*, double*, double*)?: > MCMCglmm.cc:228: warning: ?pvLS? may be used uninitialized in this function > MCMCglmm.cc:227: warning: ?pvLL? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?Lrv? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?pmuL? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?pvL? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?LambdaX? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?bv_tmp? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?bv? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?A? may be used uninitialized in this function > MCMCglmm.cc:86: warning: ?dimG? may be used uninitialized in this function > MCMCglmm.cc:228: warning: ?AlphainvS? may be used uninitialized in > this function > MCMCglmm.cc:227: warning: ?AlphainvL? may be used uninitialized in > this function > MCMCglmm.cc:225: warning: ?alphalocation_tmp? may be used > uninitialized in this function > MCMCglmm.cc:225: warning: ?alphalocation? may be used uninitialized in > this function > MCMCglmm.cc:225: warning: ?alphazstar? may be used uninitialized in > this function > MCMCglmm.cc:225: warning: ?alphapred? may be used uninitialized in > this function > MCMCglmm.cc:225: warning: ?alphaastar? may be used uninitialized in > this function > MCMCglmm.cc:225: warning: ?muAlpha? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?Alphainv? may be used uninitialized in this > function > MCMCglmm.cc:225: warning: ?tXalpha? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?Xalpha? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?linky_orig? may be used uninitialized in > this function > MCMCglmm.cc:228: warning: ?tYKrinvYS? may be used uninitialized in > this function > MCMCglmm.cc:228: warning: ?LambdaS? may be used uninitialized in this function > MCMCglmm.cc:227: warning: ?tYKrinvYL? may be used uninitialized in > this function > MCMCglmm.cc:227: warning: ?LambdaLU? may be used uninitialized in this > function > MCMCglmm.cc:225: warning: ?tYKrinvY? may be used uninitialized in this > function > MCMCglmm.cc:225: warning: ?tYKrinv? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?ILY? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?tY? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?Y? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?I? may be used uninitialized in this function > MCMCglmm.cc:228: warning: ?alphaS? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?alphaMME? may be used uninitialized in this > function > MCMCglmm.cc:225: warning: ?alphaM? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?XtmKRinv? may be used uninitialized in this > function > MCMCglmm.cc:227: warning: ?alphaL? may be used uninitialized in this function > MCMCglmm.cc:227: warning: ?L? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?alphaastar_tmp? may be used uninitialized > in this function > MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this function > MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in > this function > MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this function > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_add.c -o cs_add.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_addR.c -o cs_addR.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_amd.c -o cs_amd.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_cbind.c -o cs_cbind.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_chol.c -o cs_chol.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_cholsol.c -o cs_cholsol.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_compress.c -o cs_compress.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_counts.c -o cs_counts.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_cov2cor.c -o cs_cov2cor.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_cumsum.c -o cs_cumsum.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_dcmvnorm.c -o cs_dcmvnorm.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_dfs.c -o cs_dfs.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_directsum.c -o cs_directsum.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_directsumupdate.c -o cs_directsumupdate.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_dmperm.c -o cs_dmperm.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_dmvnorm.c -o cs_dmvnorm.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_droptol.c -o cs_droptol.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_dropzeros.c -o cs_dropzeros.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_dupl.c -o cs_dupl.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_entry.c -o cs_entry.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_ereach.c -o cs_ereach.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_etree.c -o cs_etree.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_fkeep.c -o cs_fkeep.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_gaxpy.c -o cs_gaxpy.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_happly.c -o cs_happly.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_house.c -o cs_house.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_inv.c -o cs_inv.o > cs_inv.c: In function ?cs_inv?: > cs_inv.c:9: warning: ?irow? may be used uninitialized in this function > cs_inv.c:9: warning: ?icol? may be used uninitialized in this function > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_invR.c -o cs_invR.o > cs_invR.c: In function ?cs_invR?: > cs_invR.c:9: warning: ?irow? may be used uninitialized in this function > cs_invR.c:9: warning: ?icol? may be used uninitialized in this function > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_ipvec.c -o cs_ipvec.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_kroneckerA.c -o cs_kroneckerA.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_kroneckerAupdate.c -o cs_kroneckerAupdate.o > cs_kroneckerAupdate.c: In function ?cs_kroneckerAupdate?: > cs_kroneckerAupdate.c:5: warning: unused variable ?Cp? > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_kroneckerH.c -o cs_kroneckerH.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_kroneckerI.c -o cs_kroneckerI.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_kroneckerIupdate.c -o cs_kroneckerIupdate.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_leaf.c -o cs_leaf.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_load.c -o cs_load.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_lsolve.c -o cs_lsolve.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_ltsolve.c -o cs_ltsolve.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_lu.c -o cs_lu.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_lusol.c -o cs_lusol.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_malloc.c -o cs_malloc.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_maxtrans.c -o cs_maxtrans.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_multiply.c -o cs_multiply.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_norm.c -o cs_norm.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_omega.c -o cs_omega.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_omegaupdate.c -o cs_omegaupdate.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_permute.c -o cs_permute.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_pinv.c -o cs_pinv.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_post.c -o cs_post.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_print.c -o cs_print.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_pvec.c -o cs_pvec.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_qr.c -o cs_qr.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_qrsol.c -o cs_qrsol.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_rCinvwishart.c -o cs_rCinvwishart.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_rR.c -o cs_rR.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_randperm.c -o cs_randperm.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_reach.c -o cs_reach.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_rinvwishart.c -o cs_rinvwishart.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_rwishart.c -o cs_rwishart.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_scatter.c -o cs_scatter.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_scc.c -o cs_scc.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_schol.c -o cs_schol.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_sortdv.c -o cs_sortdv.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_spsolve.c -o cs_spsolve.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_sqr.c -o cs_sqr.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_symperm.c -o cs_symperm.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_tdfs.c -o cs_tdfs.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_tmultiplyupdate.c -o cs_tmultiplyupdate.o > cs_tmultiplyupdate.c: In function ?cs_tmultiplyupdate?: > cs_tmultiplyupdate.c:16: warning: unused variable ?Cx? > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_transpose.c -o cs_transpose.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_updown.c -o cs_updown.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_usolve.c -o cs_usolve.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_util.c -o cs_util.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > cs_utsolve.c -o cs_utsolve.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > dcutopints.c -o dcutopints.o > g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c inverseA.cc -o > inverseA.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > lpzF.c -o lpzF.o > g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c rIW.cc -o rIW.o > g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c rbv.cc -o rbv.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c > rtnorm.c -o rtnorm.o > g++ -m64 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe > -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c rtnormR.cc -o rtnormR.o > g++ -m64 -shared -L/usr/local/lib64 -o MCMCglmm.so MCMCglmm.o cs_add.o > cs_addR.o cs_amd.o cs_cbind.o cs_chol.o cs_cholsol.o cs_compress.o > cs_counts.o cs_cov2cor.o cs_cumsum.o cs_dcmvnorm.o cs_dfs.o > cs_directsum.o cs_directsumupdate.o cs_dmperm.o cs_dmvnorm.o > cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o > cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o cs_house.o cs_inv.o > cs_invR.o cs_ipvec.o cs_kroneckerA.o cs_kroneckerAupdate.o > cs_kroneckerH.o cs_kroneckerI.o cs_kroneckerIupdate.o cs_leaf.o > cs_load.o cs_lsolve.o cs_ltsolve.o cs_lu.o cs_lusol.o cs_malloc.o > cs_maxtrans.o cs_multiply.o cs_norm.o cs_omega.o cs_omegaupdate.o > cs_permute.o cs_pinv.o cs_post.o cs_print.o cs_pvec.o cs_qr.o > cs_qrsol.o cs_rCinvwishart.o cs_rR.o cs_randperm.o cs_reach.o > cs_rinvwishart.o cs_rwishart.o cs_scatter.o cs_scc.o cs_schol.o > cs_sortdv.o cs_spsolve.o cs_sqr.o cs_symperm.o cs_tdfs.o > cs_tmultiplyupdate.o cs_transpose.o cs_updown.o cs_usolve.o cs_util.o > cs_utsolve.o dcutopints.o inverseA.o lpzF.o rIW.o rbv.o rtnorm.o > rtnormR.o -L/usr/lib64/R/lib -lR > ** R > ** data > ** inst > ** preparing package for lazy loading > Loading required package: lattice > Attaching package: 'Matrix' > The following object(s) are masked from package:tensorA : > norm > The following object(s) are masked from package:stats : > contr.SAS, > contr.helmert, > contr.poly, > contr.sum, > contr.treatment, > xtabs > The following object(s) are masked from package:base : > rcond > ** help > *** installing help indices >>>> Building/Updating help pages for package 'MCMCglmm' > Formats: text html latex example > BTdata text html latex > BTped text html latex > Ddivergence text html latex example > Dexpressions text html latex > Dtensor text html latex example > KPPM text html latex example > MCMCglmm text html latex example > MCMCglmmPackage text html latex > PlodiaPO text html latex > PlodiaR text html latex > PlodiaRB text html latex > Ptensor text html latex example > SShorns text html latex > Tri2M text html latex example > at.level text html latex example > at.set text html latex example > commutation text html latex example > evalDtensor text html latex example > inverseA text html latex example > knorm text html latex example > krzanowski.test text html latex example > kunif text html latex example > leg text html latex example > list2bdiag text html latex example > mult.memb text html latex example > plot.MCMCglmm text html latex > plotsubspace text html latex example > posterior.cor text html latex example > posterior.evals text html latex example > posterior.mode text html latex example > predict.MCMCglmm text html latex > prunePed text html latex > rIW text html latex example > rbv text html latex example > residuals.MCMCglmm text html latex > rtnorm text html latex example > sir text html latex example > sm2asreml text html latex example > spl text html latex example > summary.MCMCglmm text html latex > ** building package indices ... > * DONE (MCMCglmm) > * creating vignettes ... OK > * cleaning src > * removing junk files > unlink MCMCglmm_2.05/R/ residuals.MCMCglmm.R > ~ > unlink MCMCglmm_2.05/R/.DS_Store > unlink MCMCglmm_2.05/R/prunePed.R > unlink MCMCglmm_2.05/R/commutation.R~ > unlink MCMCglmm_2.05/R/rtnorm.R~ > unlink MCMCglmm_2.05/R/KPPM.R~ > unlink MCMCglmm_2.05/R/cs_inversion.c~ > unlink MCMCglmm_2.05/R/posterior.cor.R > unlink MCMCglmm_2.05/R/Ddivergence.R~ > unlink MCMCglmm_2.05/R/posterior.evals.R > unlink MCMCglmm_2.05/R/rbv.R~ > unlink MCMCglmm_2.05/R/rbv.R > unlink MCMCglmm_2.05/R/plot.prior.R~ > unlink MCMCglmm_2.05/R/predict.MCMCglmm.R > unlink MCMCglmm_2.05/R/sm2asreml.R~ > unlink MCMCglmm_2.05/R/Lweib.R~ > unlink MCMCglmm_2.05/R/plot.MCMCglmm.R > unlink MCMCglmm_2.05/R/krzanowski.test.R > unlink MCMCglmm_2.05/R/Fdivergence.R~ > unlink MCMCglmm_2.05/R/sir.R~ > unlink MCMCglmm_2.05/R/summary.MCMCglmm.R > unlink MCMCglmm_2.05/R/mult.memb.R > unlink MCMCglmm_2.05/R/predict.MCMCglmm.R~ > unlink MCMCglmm_2.05/R/KPPM.R > unlink MCMCglmm_2.05/R/spl.R > unlink MCMCglmm_2.05/R/Dtensor.R > unlink MCMCglmm_2.05/R/Ptensor.R > unlink MCMCglmm_2.05/R/kunif.R > unlink MCMCglmm_2.05/R/residuals.MCMCglmm.R > unlink MCMCglmm_2.05/R/mult.memb.R~ > unlink MCMCglmm_2.05/R/knorm.R > unlink MCMCglmm_2.05/R/MCMCglmm.R~ > unlink MCMCglmm_2.05/R/MCMCglmm.R > unlink MCMCglmm_2.05/R/SimL.R~ > unlink MCMCglmm_2.05/R/list2bdiag.R > unlink MCMCglmm_2.05/R/mterms.R~ > unlink MCMCglmm_2.05/R/prunePed.R~ > unlink MCMCglmm_2.05/R/sm2asreml.R > unlink MCMCglmm_2.05/R/plotsubspace.R > unlink MCMCglmm_2.05/R/plot.MCMCglmm.R~ > unlink MCMCglmm_2.05/R/residuals.MCMCglmm.R~ > unlink MCMCglmm_2.05/R/Ecor.R~ > unlink MCMCglmm_2.05/R/commutation.R > unlink MCMCglmm_2.05/R/getVCV.R~ > unlink MCMCglmm_2.05/R/asreml.R~ > unlink MCMCglmm_2.05/R/pretty.R~ > unlink MCMCglmm_2.05/R/sir.R > unlink MCMCglmm_2.05/R/rIW.R > unlink MCMCglmm_2.05/R/split.direct.sum.R~ > unlink MCMCglmm_2.05/R/Tri2M.R > unlink MCMCglmm_2.05/R/find.componets.R~ > unlink MCMCglmm_2.05/R/inverseA.R > unlink MCMCglmm_2.05/R/MCMCam.R~ > unlink MCMCglmm_2.05/R/inverseAnonC.R~ > unlink MCMCglmm_2.05/R/posterior.mode.R > unlink MCMCglmm_2.05/R/path.R~ > unlink MCMCglmm_2.05/R/rIW.R~ > unlink MCMCglmm_2.05/R/knorm.R~ > unlink MCMCglmm_2.05/R/Dtensor.R~ > unlink MCMCglmm_2.05/R/buildZ.R~ > unlink MCMCglmm_2.05/R/plotsubspace.R~ > unlink MCMCglmm_2.05/R/posterior.mode.R~ > unlink MCMCglmm_2.05/R/posterior.cor.R~ > unlink MCMCglmm_2.05/R/split.direct.sum.R > unlink MCMCglmm_2.05/R/residuals (copy).MCMCglmm.R~ > unlink MCMCglmm_2.05/R/Dexpressions.R~ > unlink MCMCglmm_2.05/R/Ddivergence.R > unlink MCMCglmm_2.05/R/spl.R~ > unlink MCMCglmm_2.05/R/Dexpressions.R > unlink MCMCglmm_2.05/R/mterms.R > unlink MCMCglmm_2.05/R/rtnorm.R > unlink MCMCglmm_2.05/R/inverseA.R~ > unlink MCMCglmm_2.05/R/find.components.R~ > unlink MCMCglmm_2.05/R/posterior.evals.R~ > unlink MCMCglmm_2.05/R/multmemb.R~ > unlink MCMCglmm_2.05/R/SStest.R~ > unlink MCMCglmm_2.05/R/plotprior.R~ > unlink MCMCglmm_2.05/R/find.components.R > unlink MCMCglmm_2.05/R/MCMCgompSInt.R~ > unlink MCMCglmm_2.05/R/dcmvnorm.R~ > unlink MCMCglmm_2.05/R/summary.MCMCglmm.R~ > unlink MCMCglmm_2.05/R/buildZ.R > rmdir MCMCglmm_2.05/R > cannot remove directory for /home/jarrod/mnt/shared: Permission denied > at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/mnt/scieng1: Permission > denied at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/mnt: Directory not empty at > /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/.gvfs: Device or resource > busy at /usr/lib64/R/bin/build line 263 > cannot make child directory read-write-exec for > /home/jarrod/.local/share/Trash/files/MasterBayes_2.2.4.Rcheck: > Operation not permitted at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/.local/share/Trash/files: > Directory not empty at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/.local/share/Trash: Directory > not empty at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/.local/share: Directory not > empty at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod/.local: Directory not empty > at /usr/lib64/R/bin/build line 263 > cannot remove directory for /home/jarrod: Permission denied at > /usr/lib64/R/bin/build line 263 > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building 'MCMCglmm_2.05.tar.gz' > tar: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: Cannot open: No such > file or directory > tar: Error is not recoverable: exiting now > gzip: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: No such file or directory > cannot remove path when cwd is /tmp/Rbuild93379662 for > /tmp/Rbuild93379662: at /usr/lib64/R/bin/build line 433 > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. 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