Re: [Rd] R CMD build wiped my computer

From: Jarrod Hadfield <j.hadfield_at_ed.ac.uk>
Date: Wed, 28 Jul 2010 11:53:31 +0100

Hi Martin,

I think this is the most likely reason given that the name in the DESCRIPTION file does NOT have a version number. Even so, it is very easy to misname a file and then delete it/change its name (as I've done here) and I hope current versions of R would not cause this problem. Perhaps Fedora should not use ~ as its back up file suffixes?

Cheers,

Jarrod

On 28 Jul 2010, at 11:41, Martin Maechler wrote:

>>>>>> Jarrod Hadfield <j.hadfield@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
>> 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_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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

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Received on Wed 28 Jul 2010 - 11:40:30 GMT

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