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
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.
>>>>> Jarrod Hadfield <j.hadfield at 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 > [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 > 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. > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel