From j.hadfield at ed.ac.uk  Tue Jul 27 22:37:09 2010
From: j.hadfield at ed.ac.uk (Jarrod Hadfield)
Date: Tue, 27 Jul 2010 21:37:09 +0100
Subject: [Rd] R CMD build wiped my computer
Message-ID: <20100727213709.q1q0u1fm4ooo880s@www.staffmail.ed.ac.uk>

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.

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
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   kunif                             text    html    latex   example
   leg                               text    html    latex   example
   list2bdiag                        text    html    latex   example
   mult.memb                         text    html    latex   example
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   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
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* checking for LF line-endings in source and make files
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gzip: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: No such file or directory
cannot remove path when cwd is /tmp/Rbuild93379662 for  
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-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



[Rd] R CMD build wiped my computer
Jarrod Hadfield