From maechler at stat.math.ethz.ch  Wed Jul 28 12:41:18 2010
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Wed, 28 Jul 2010 12:41:18 +0200
Subject: [Rd] R CMD build wiped my computer
In-Reply-To: <20100727213709.q1q0u1fm4ooo880s@www.staffmail.ed.ac.uk>
References: <20100727213709.q1q0u1fm4ooo880s@www.staffmail.ed.ac.uk>
Message-ID: <19536.2382.89915.942133@cmath-5.math.ethz.ch>

>>>>> 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
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    > 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
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    > 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



[Rd] R CMD build wiped my computer
Martin Maechler