Hi Martin,
I think this is the most likely reason given that the name in the
DESCRIPTION file does NOT have a version number. Even so, it is very
easy to misname a file and then delete it/change its name (as I've
done here) and I hope current versions of R would not cause this
problem. Perhaps Fedora should not use ~ as its back up file suffixes?
Cheers,
Jarrod
On 28 Jul 2010, at 11:41, Martin Maechler wrote:
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).
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 :
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** help
*** installing help indices
Building/Updating help pages for package 'MCMCglmm'
Formats: text html latex example
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--
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