Re: [Rd] R CMD build wiped my computer

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Wed, 28 Jul 2010 12:41:18 +0200

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

> Attaching package: 'Matrix'

> The following object(s) are masked from package:tensorA :

> norm

> The following object(s) are masked from package:stats :

> contr.SAS,
> contr.helmert,
> contr.poly,
> contr.sum,
> contr.treatment,
> xtabs

> The following object(s) are masked from package:base :

> rcond

> ** help
> *** installing help indices

    >>>> Building/Updating help pages for package 'MCMCglmm'

> Formats: text html latex example
> BTdata text html latex
> BTped text html latex
> Ddivergence text html latex example
> Dexpressions text html latex
> Dtensor text html latex example
> KPPM text html latex example
> MCMCglmm text html latex example
> MCMCglmmPackage text html latex
> PlodiaPO text html latex
> PlodiaR text html latex
> PlodiaRB text html latex
> Ptensor text html latex example
> SShorns text html latex
> Tri2M text html latex example
> at.level text html latex example
> at.set text html latex example
> commutation text html latex example
> evalDtensor text html latex example
> inverseA text html latex example
> knorm text html latex example
> krzanowski.test text html latex example
> kunif text html latex example
> leg text html latex example
> list2bdiag text html latex example
> mult.memb text html latex example
> plot.MCMCglmm text html latex
> plotsubspace text html latex example
> posterior.cor text html latex example
> posterior.evals text html latex example
> posterior.mode text html latex example
> predict.MCMCglmm text html latex
> prunePed text html latex
> rIW text html latex example
> rbv text html latex example
> residuals.MCMCglmm text html latex
> rtnorm text html latex example
> sir text html latex example
> sm2asreml text html latex example
> spl text html latex example
> summary.MCMCglmm text html latex
> ** building package indices ...
> * DONE (MCMCglmm)
> * creating vignettes ... OK
> * cleaning src
> * removing junk files
> unlink MCMCglmm_2.05/R/ residuals.MCMCglmm.R
> ~
> unlink MCMCglmm_2.05/R/.DS_Store
> unlink MCMCglmm_2.05/R/prunePed.R
> unlink MCMCglmm_2.05/R/commutation.R~
> unlink MCMCglmm_2.05/R/rtnorm.R~
> unlink MCMCglmm_2.05/R/KPPM.R~
> unlink MCMCglmm_2.05/R/cs_inversion.c~
> unlink MCMCglmm_2.05/R/posterior.cor.R
> unlink MCMCglmm_2.05/R/Ddivergence.R~
> unlink MCMCglmm_2.05/R/posterior.evals.R
> unlink MCMCglmm_2.05/R/rbv.R~
> unlink MCMCglmm_2.05/R/rbv.R
> unlink MCMCglmm_2.05/R/plot.prior.R~
> unlink MCMCglmm_2.05/R/predict.MCMCglmm.R
> unlink MCMCglmm_2.05/R/sm2asreml.R~
> unlink MCMCglmm_2.05/R/Lweib.R~
> unlink MCMCglmm_2.05/R/plot.MCMCglmm.R
> unlink MCMCglmm_2.05/R/krzanowski.test.R
> unlink MCMCglmm_2.05/R/Fdivergence.R~
> unlink MCMCglmm_2.05/R/sir.R~
> unlink MCMCglmm_2.05/R/summary.MCMCglmm.R
> unlink MCMCglmm_2.05/R/mult.memb.R
> unlink MCMCglmm_2.05/R/predict.MCMCglmm.R~
> unlink MCMCglmm_2.05/R/KPPM.R
> unlink MCMCglmm_2.05/R/spl.R
> unlink MCMCglmm_2.05/R/Dtensor.R
> unlink MCMCglmm_2.05/R/Ptensor.R
> unlink MCMCglmm_2.05/R/kunif.R
> unlink MCMCglmm_2.05/R/residuals.MCMCglmm.R
> unlink MCMCglmm_2.05/R/mult.memb.R~
> unlink MCMCglmm_2.05/R/knorm.R
> unlink MCMCglmm_2.05/R/MCMCglmm.R~
> unlink MCMCglmm_2.05/R/MCMCglmm.R
> unlink MCMCglmm_2.05/R/SimL.R~
> unlink MCMCglmm_2.05/R/list2bdiag.R
> unlink MCMCglmm_2.05/R/mterms.R~
> unlink MCMCglmm_2.05/R/prunePed.R~
> unlink MCMCglmm_2.05/R/sm2asreml.R
> unlink MCMCglmm_2.05/R/plotsubspace.R
> unlink MCMCglmm_2.05/R/plot.MCMCglmm.R~
> unlink MCMCglmm_2.05/R/residuals.MCMCglmm.R~
> unlink MCMCglmm_2.05/R/Ecor.R~
> unlink MCMCglmm_2.05/R/commutation.R
> unlink MCMCglmm_2.05/R/getVCV.R~
> unlink MCMCglmm_2.05/R/asreml.R~
> unlink MCMCglmm_2.05/R/pretty.R~
> unlink MCMCglmm_2.05/R/sir.R
> unlink MCMCglmm_2.05/R/rIW.R
> unlink MCMCglmm_2.05/R/split.direct.sum.R~
> unlink MCMCglmm_2.05/R/Tri2M.R
> unlink MCMCglmm_2.05/R/find.componets.R~
> unlink MCMCglmm_2.05/R/inverseA.R
> unlink MCMCglmm_2.05/R/MCMCam.R~
> unlink MCMCglmm_2.05/R/inverseAnonC.R~
> unlink MCMCglmm_2.05/R/posterior.mode.R
> unlink MCMCglmm_2.05/R/path.R~
> unlink MCMCglmm_2.05/R/rIW.R~
> unlink MCMCglmm_2.05/R/knorm.R~
> unlink MCMCglmm_2.05/R/Dtensor.R~
> unlink MCMCglmm_2.05/R/buildZ.R~
> unlink MCMCglmm_2.05/R/plotsubspace.R~
> unlink MCMCglmm_2.05/R/posterior.mode.R~
> unlink MCMCglmm_2.05/R/posterior.cor.R~
> unlink MCMCglmm_2.05/R/split.direct.sum.R
> unlink MCMCglmm_2.05/R/residuals (copy).MCMCglmm.R~
> unlink MCMCglmm_2.05/R/Dexpressions.R~
> unlink MCMCglmm_2.05/R/Ddivergence.R
> unlink MCMCglmm_2.05/R/spl.R~
> unlink MCMCglmm_2.05/R/Dexpressions.R
> unlink MCMCglmm_2.05/R/mterms.R
> unlink MCMCglmm_2.05/R/rtnorm.R
> unlink MCMCglmm_2.05/R/inverseA.R~
> unlink MCMCglmm_2.05/R/find.components.R~
> unlink MCMCglmm_2.05/R/posterior.evals.R~
> unlink MCMCglmm_2.05/R/multmemb.R~
> unlink MCMCglmm_2.05/R/SStest.R~
> unlink MCMCglmm_2.05/R/plotprior.R~
> unlink MCMCglmm_2.05/R/find.components.R
> unlink MCMCglmm_2.05/R/MCMCgompSInt.R~
> unlink MCMCglmm_2.05/R/dcmvnorm.R~
> unlink MCMCglmm_2.05/R/summary.MCMCglmm.R~
> unlink MCMCglmm_2.05/R/buildZ.R
> rmdir MCMCglmm_2.05/R
> cannot remove directory for /home/jarrod/mnt/shared: Permission denied
> at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/mnt/scieng1: Permission
> denied at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/mnt: Directory not empty at
> /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/.gvfs: Device or resource
> busy at /usr/lib64/R/bin/build line 263
> cannot make child directory read-write-exec for
> /home/jarrod/.local/share/Trash/files/MasterBayes_2.2.4.Rcheck:
> Operation not permitted at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/.local/share/Trash/files:
> Directory not empty at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/.local/share/Trash: Directory
> not empty at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/.local/share: Directory not
> empty at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod/.local: Directory not empty
> at /usr/lib64/R/bin/build line 263
> cannot remove directory for /home/jarrod: Permission denied at
> /usr/lib64/R/bin/build line 263
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building 'MCMCglmm_2.05.tar.gz'
> tar: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: Cannot open: No such
> file or directory
> tar: Error is not recoverable: exiting now
> gzip: /home/jarrod/Work/AManal/MCMCglmm_2.05.tar: No such file or directory
> cannot remove path when cwd is /tmp/Rbuild93379662 for
> /tmp/Rbuild93379662: at /usr/lib64/R/bin/build line 433

> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Wed 28 Jul 2010 - 10:46:19 GMT

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