Re: [R] R CMD build wiped my computer

[Duncan Murdoch]

Jarrod Hadfield wrote:
Hi,
Thanks for your responses. Although a wrist slapping for not keeping  
updated with R/Fedora may be warranted,  I find it quite terrifying  
that by simply having a version number in a directory name R went on  
to try and erase everything on the computer! Thank god I wasn't logged  
in as root.
  

I also find that upsetting, but believe me, it's not true about current 
versions -- I tried it.  I don't have a copy of 2.9.0 around to try, but 
I would assume this is a bug in that version that has been fixed, or 
possibly something very weird about your system (e.g. files linked in a 
strange way).

By the way, in current versions you could get away with naming the 
directory as MCMCglmm_2.05, just not the package (whose name is taken 
from the DESCRIPTION file).  Doing that will give you an error about a 
malformed package name.
Anyway, the more pressing issue is what I can do about this. My main  
concern is recovering those changes that were made to the package  
prior to its deletion. Luckily, just before running R CMD build I ran  
R CMD install under root (hence my belief I had ran R CMD build under  
root). I also have an open terminal for which the current package is  
loaded (and working I think). My question is how and how much can be  
recovered from this - having the C/C++ code would be particularly  
useful.

  

You can likely recover deparsed versions of the R code, but the C/C++ 
code is not installed, only compiled versions of it are.  To recover 
that you need to do things outside of R, and you probably needed to set 
those up in advance of your disaster.

If you were using 2.10.0 or newer, you'd be able to recover the source 
to your man pages.  With 2.9.0, I think you'll have to do a lot of 
manual editing to get them back.

Files like DESCRIPTION and NAMESPACE are installed (with some small 
additions to DESCRIPTION), so they'll be easy to recover.

Duncan Murdoch

Cheers,

Jarrod


On 27 Jul 2010, at 22:53, Duncan Murdoch wrote:

  
On 27/07/2010 4:39 PM, Jarrod Hadfield wrote:
    
Hi,
I ran R (version 2.9.0) CMD build under root in Fedora (9). When it
tried to remove "junk files" it removed EVERYTHING in my local
account! (See below).
Can anyone tell me what happened, and even more importantly if I  
can I
restore what was lost.
      
You did several things you shouldn't have done.  Don't run as root  
unless you need to do what root can do.  R CMD build shouldn't need  
special permissions, so it shouldn't be run as root.  (Actually, it  
looks as though you didn't run as root: you got a number of  
"permissions denied" messages.)

And don't run obsolete versions of R.  There have been a lot of bug  
fixes since 2.9.0; you should take advantage of them.

You should have known those two.  One thing you might not have known  
is that it's a bad idea to name a package with the version number in  
the directory name.  I don't think this will cause a lot of trouble  
with current versions of R, but it won't work.  Apparently in 2.9.0  
it caused  a lot of trouble.

Basically you need to restore from your backup.  If you don't have  
one, you just learned how important Davidson's laws of computing are:

The First Law: Back it up.

The Second Law:  Do it now.

It may not sound like it, but I am sympathetic.

Duncan Murdoch


    
Panickingly,
Jarrod
[jar...@localhost AManal]$ R CMD build MCMCglmm_2.05
* checking for file 'MCMCglmm_2.05/DESCRIPTION' ... OK
* preparing 'MCMCglmm_2.05':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package ?MCMCglmm? ...
** libs
g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g - 
pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c MCMCglmm.cc -o
MCMCglmm.o
MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*,
int*, int*, int*, int*, int*, int*, double*, int*, int*, double*,
int*, int*, double*, double*, int*, int*, int*, int*, int*, int*,
int*, int*, int*, int*, double*, double*, double*, int*, int*, int*,
int*, double*, double*, double*, int*, double*, bool*, double*,
double*, int*, int*, int*, int*, int*, double*, int*, int*, int*,
double*, double*, double*, int*, int*, double*, int*, int*, int*,
int*, double*, double*, double*, double*)?:
MCMCglmm.cc:228: warning: ?pvLS? may be used uninitialized in this  
function
MCMCglmm.cc:227: warning: ?pvLL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?Lrv? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?pmuL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?pvL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?LambdaX? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?bv_tmp? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?bv? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?A? may be used uninitialized in this  
function
MCMCglmm.cc:86: warning: ?dimG? may be used uninitialized in this  
function
MCMCglmm.cc:228: warning: ?AlphainvS? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?AlphainvL? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphalocation_tmp? may be used
uninitialized in this function
MCMCglmm.cc:225: warning: ?alphalocation? may be used uninitialized  
in
this function
MCMCglmm.cc:225: warning: ?alphazstar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphapred? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphaastar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?muAlpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?Alphainv? may be used uninitialized in  
this
function
MCMCglmm.cc:225: warning: ?tXalpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?Xalpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?linky_orig? may be used uninitialized in
this function
MCMCglmm.cc:228: warning: ?tYKrinvYS? may be used uninitialized in
this function
MCMCglmm.cc:228: warning: ?LambdaS? may be used uninitialized in  
this function
MCMCglmm.cc:227: warning: ?tYKrinvYL? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?LambdaLU? may be used uninitialized in  
this
function
MCMCglmm.cc:225: warning: ?tYKrinvY? may be used uninitialized in  
this
function
MCMCglmm.cc:225: warning: ?tYKrinv? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?ILY? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?tY? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?Y? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?I? may be used uninitialized in this  
function
MCMCglmm.cc:228: warning: ?alphaS? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?alphaMME? may be used uninitialized in  
this
function
MCMCglmm.cc:225: warning: ?alphaM? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?XtmKRinv? may be used uninitialized in  
this
function
MCMCglmm.cc:227: warning: ?alphaL? may be used uninitialized in  
this function
MCMCglmm.cc:227: warning: ?L? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?alphaastar_tmp? may be used uninitialized
in this function
MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this  
function
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_add.c -o cs_add.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_addR.c -o cs_addR.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_amd.c -o cs_amd.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_cbind.c -o cs_cbind.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_chol.c -o cs_chol.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_cholsol.c -o cs_cholsol.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_compress.c -o cs_compress.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_counts.c -o cs_counts.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_cov2cor.c -o cs_cov2cor.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_cumsum.c -o cs_cumsum.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_dcmvnorm.c -o cs_dcmvnorm.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_dfs.c -o cs_dfs.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_directsum.c -o cs_directsum.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_directsumupdate.c -o cs_directsumupdate.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_dmperm.c -o cs_dmperm.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_dmvnorm.c -o cs_dmvnorm.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_droptol.c -o cs_droptol.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_dropzeros.c -o cs_dropzeros.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_dupl.c -o cs_dupl.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_entry.c -o cs_entry.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_ereach.c -o cs_ereach.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_etree.c -o cs_etree.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_fkeep.c -o cs_fkeep.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_gaxpy.c -o cs_gaxpy.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_happly.c -o cs_happly.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_house.c -o cs_house.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_inv.c -o cs_inv.o
cs_inv.c: In function ?cs_inv?:
cs_inv.c:9: warning: ?irow? may be used uninitialized in this  
function
cs_inv.c:9: warning: ?icol? may be used uninitialized in this  
function
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_invR.c -o cs_invR.o
cs_invR.c: In function ?cs_invR?:
cs_invR.c:9: warning: ?irow? may be used uninitialized in this  
function
cs_invR.c:9: warning: ?icol? may be used uninitialized in this  
function
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_ipvec.c -o cs_ipvec.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_kroneckerA.c -o cs_kroneckerA.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_kroneckerAupdate.c -o cs_kroneckerAupdate.o
cs_kroneckerAupdate.c: In function ?cs_kroneckerAupdate?:
cs_kroneckerAupdate.c:5: warning: unused variable ?Cp?
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_kroneckerH.c -o cs_kroneckerH.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_kroneckerI.c -o cs_kroneckerI.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_kroneckerIupdate.c -o cs_kroneckerIupdate.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_leaf.c -o cs_leaf.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_load.c -o cs_load.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_lsolve.c -o cs_lsolve.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_ltsolve.c -o cs_ltsolve.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_lu.c -o cs_lu.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_lusol.c -o cs_lusol.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_malloc.c -o cs_malloc.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_maxtrans.c -o cs_maxtrans.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_multiply.c -o cs_multiply.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_norm.c -o cs_norm.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_omega.c -o cs_omega.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_omegaupdate.c -o cs_omegaupdate.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_permute.c -o cs_permute.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_pinv.c -o cs_pinv.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_post.c -o cs_post.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_print.c -o cs_print.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_pvec.c -o cs_pvec.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_qr.c -o cs_qr.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_qrsol.c -o cs_qrsol.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_rCinvwishart.c -o cs_rCinvwishart.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_rR.c -o cs_rR.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_randperm.c -o cs_randperm.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_reach.c -o cs_reach.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_rinvwishart.c -o cs_rinvwishart.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_rwishart.c -o cs_rwishart.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_scatter.c -o cs_scatter.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_scc.c -o cs_scc.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_schol.c -o cs_schol.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_sortdv.c -o cs_sortdv.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_spsolve.c -o cs_spsolve.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_sqr.c -o cs_sqr.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_symperm.c -o cs_symperm.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_tdfs.c -o cs_tdfs.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_tmultiplyupdate.c -o cs_tmultiplyupdate.o
cs_tmultiplyupdate.c: In function ?cs_tmultiplyupdate?:
cs_tmultiplyupdate.c:16: warning: unused variable ?Cx?
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_transpose.c -o cs_transpose.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_updown.c -o cs_updown.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_usolve.c -o cs_usolve.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_util.c -o cs_util.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_utsolve.c -o cs_utsolve.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
dcutopints.c -o dcutopints.o
g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g - 
pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c inverseA.cc -o
inverseA.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
lpzF.c -o lpzF.o
g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g - 
pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c rIW.cc -o rIW.o
g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g - 
pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c rbv.cc -o rbv.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include    -fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
rtnorm.c -o rtnorm.o
g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g - 
pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c rtnormR.cc -o  
rtnormR.o
g++ -m64 -shared -L/usr/local/lib64 -o MCMCglmm.so MCMCglmm.o  
cs_add.o
cs_addR.o cs_amd.o cs_cbind.o cs_chol.o cs_cholsol.o cs_compress.o
cs_counts.o cs_cov2cor.o cs_cumsum.o cs_dcmvnorm.o cs_dfs.o
cs_directsum.o cs_directsumupdate.o cs_dmperm.o cs_dmvnorm.o
cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o
cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o cs_house.o cs_inv.o
cs_invR.o cs_ipvec.o cs_kroneckerA.o cs_kroneckerAupdate.o
cs_kroneckerH.o cs_kroneckerI.o cs_kroneckerIupdate.o cs_leaf.o
cs_load.o cs_lsolve.o cs_ltsolve.o cs_lu.o cs_lusol.o cs_malloc.o
cs_maxtrans.o cs_multiply.o cs_norm.o cs_omega.o cs_omegaupdate.o
cs_permute.o cs_pinv.o cs_post.o cs_print.o cs_pvec.o cs_qr.o
cs_qrsol.o cs_rCinvwishart.o cs_rR.o cs_randperm.o cs_reach.o
cs_rinvwishart.o cs_rwishart.o cs_scatter.o cs_scc.o cs_schol.o
cs_sortdv.o cs_spsolve.o cs_sqr.o cs_symperm.o cs_tdfs.o
cs_tmultiplyupdate.o cs_transpose.o cs_updown.o cs_usolve.o cs_util.o
cs_utsolve.o dcutopints.o inverseA.o lpzF.o rIW.o rbv.o rtnorm.o
rtnormR.o -L/usr/lib64/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: lattice
Attaching package: 'Matrix'
        The following object(s) are masked from package:tensorA :
         norm
        The following object(s) are masked from package:stats :
         contr.SAS,
         contr.helmert,
         contr.poly,
         contr.sum,
         contr.treatment,
         xtabs
        The following object(s) are masked from package:base :
         rcond
** help
*** installing help indices
  >>> Building/Updating help pages for package 'MCMCglmm'
      Formats: text html latex example
   BTdata                            text    html    latex
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   knorm                             text    html    latex   example
   krzanowski.test                   text    html    latex   example
   kunif                             text    html    latex   example
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   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
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