On 27/07/2010 4:39 PM, Jarrod Hadfield wrote:> 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, and even more importantly if I can I
> restore what was lost.
You did several things you shouldn't have done. Don't run as root
unless you need to do what root can do. R CMD build shouldn't need
special permissions, so it shouldn't be run as root. (Actually, it
looks as though you didn't run as root: you got a number of
"permissions
denied" messages.)
And don't run obsolete versions of R. There have been a lot of bug
fixes since 2.9.0; you should take advantage of them.
You should have known those two. One thing you might not have known is
that it's a bad idea to name a package with the version number in the
directory name. I don't think this will cause a lot of trouble with
current versions of R, but it won't work. Apparently in 2.9.0 it caused
a lot of trouble.
Basically you need to restore from your backup. If you don't have one,
you just learned how important Davidson's laws of computing are:
The First Law: Back it up.
The Second Law: Do it now.
It may not sound like it, but I am sympathetic.
Duncan Murdoch
>
> Panickingly,
>
> Jarrod
>
> [jarrod at 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
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> 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
> ~
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> 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:
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> not empty at /usr/lib64/R/bin/build line 263
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> 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
>
>