[R] R CMD build wiped my computer

Duncan Murdoch murdoch.duncan at gmail.com
Wed Jul 28 12:24:57 CEST 2010


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
>>> [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~
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>>> unlink MCMCglmm_2.05/R/rIW.R
>>> unlink MCMCglmm_2.05/R/split.direct.sum.R~
>>> unlink MCMCglmm_2.05/R/Tri2M.R
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>>> 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~
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>>> unlink MCMCglmm_2.05/R/multmemb.R~
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>>> 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
>>>       
>>     
>
>
>



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