[R] 3.0.1 update and compiler package
Christoph Knapp
christoph.knapp01 at gmail.com
Tue Jun 4 10:41:21 CEST 2013
Hi,
reinstalling R did not help. It still will not update the same packages.
I attached the terminal output. There were no errors while I was
installing R again. I might have to remove all libraries and reinstall
them all. Would you agree or do you think I should try something else
first which is not as extreme.
Thanks for your help
Christoph
On 03/06/13 20:32, Pascal Oettli wrote:
> My mistake,
>
> Regards,
> Pascal
>
> On 06/03/2013 04:37 PM, Uwe Ligges wrote:
>>
>>
>> On 03.06.2013 07:19, Pascal Oettli wrote:
>>> Hi,
>>>
>>> How did you upgraded your version of R? From source or from a Linux
>>> package?
>>
>> Actually the new R installation is just broken. It simply has to be
>> reinstalled carefully (watch for errors).
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>>
>>>
>>> Regards,
>>> Pascal
>>>
>>>
>>> On 05/31/2013 11:33 AM, Christoph Knapp wrote:
>>>> Hi,
>>>> I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I
>>>> realized that I have to update all the installed packages so I run >
>>>> update.packages(checkBuilt=TRUE)
>>>> as described here
>>>> http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/
>>>>
>>>>
>>>>
>>>> . The first thing it did was telling me that it will not update
>>>> several
>>>> packages. When it was finished I used the warnings function to have a
>>>> look at what did not work. See the list below.
>>>>
>>>> > warnings()
>>>> Warning messages:
>>>> 1: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘boot’ had non-zero exit status
>>>> 2: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘cluster’ had non-zero exit status
>>>> 3: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘foreign’ had non-zero exit status
>>>> 4: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘KernSmooth’ had non-zero exit status
>>>> 5: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘MASS’ had non-zero exit status
>>>> 6: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘Matrix’ had non-zero exit status
>>>> 7: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘nlme’ had non-zero exit status
>>>> 8: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘nnet’ had non-zero exit status
>>>> 9: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘rpart’ had non-zero exit status
>>>> 10: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘spatial’ had non-zero exit status
>>>> 11: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘survival’ had non-zero exit status
>>>> 12: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘class’ had non-zero exit status
>>>> 13: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘epiR’ had non-zero exit status
>>>> 14: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘gmodels’ had non-zero exit status
>>>> 15: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘gplots’ had non-zero exit status
>>>> 16: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘mgcv’ had non-zero exit status
>>>> 17: In install.packages(update[instlib == l, "Package"], l, ... :
>>>> installation of package ‘gregmisc’ had non-zero exit status
>>>>
>>>> I tried to reinstall them manually but this always failed because of a
>>>> package dependency to the "compiler" package. Now, if I try to install
>>>> the compiler package it tells me.
>>>>
>>>> > install.packages("compiler")
>>>> Installing package into
>>>> ‘/home/christoph/R/x86_64-pc-linux-gnu-library/3.0’
>>>> (as ‘lib’ is unspecified)
>>>> Warning message:
>>>> package ‘compiler’ is not available (for R version 3.0.1)
>>>>
>>>> The last line also came up all the time when the packages were updated
>>>>
>>>> Doing a bit of research does not deliver much only that the compiler
>>>> package was included into R at version 2.13.0
>>>> (http://dirk.eddelbuettel.com/blog/2011/04/12/).
>>>>
>>>> Most of those packages which do not work any more are pretty important
>>>> for some of my scripts and I would not even know what packages replace
>>>> the packages above.
>>>>
>>>> Would anyone know how to fix this?
>>>>
>>>> Regards
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
-------------- next part --------------
christoph at christoph-Latitude-E4300:~$ sudo apt-get --purge remove r-base-core
[sudo] password for christoph:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED
r-base* r-base-core* r-base-dev* r-base-html* r-cran-boot* r-cran-class*
r-cran-cluster* r-cran-codetools* r-cran-foreign* r-cran-kernsmooth*
r-cran-lattice* r-cran-mass* r-cran-matrix* r-cran-mgcv* r-cran-nlme*
r-cran-nnet* r-cran-rpart* r-cran-spatial* r-cran-survival* r-recommended*
0 upgraded, 0 newly installed, 20 to remove and 20 not upgraded.
After this operation, 51.5 MB disk space will be freed.
Do you want to continue [Y/n]? Y
(Reading database ... 429389 files and directories currently installed.)
Removing r-base ...
Removing r-recommended ...
Removing r-cran-boot ...
Removing r-cran-mgcv ...
Removing r-cran-matrix ...
Removing r-cran-rpart ...
Removing r-cran-survival ...
Removing r-cran-kernsmooth ...
Removing r-base-dev ...
Removing r-cran-spatial ...
Removing r-cran-cluster ...
Removing r-cran-class ...
Removing r-cran-foreign ...
Removing r-cran-nlme ...
Removing r-cran-nnet ...
Removing r-base-html ...
Removing r-cran-lattice ...
Removing r-cran-mass ...
Removing r-cran-codetools ...
Removing r-base-core ...
Purging configuration files for r-base-core ...
dpkg: warning: while removing r-base-core, directory '/usr/lib/R/library' not empty so not removed.
dpkg: warning: while removing r-base-core, directory '/usr/lib/R/site-library' not empty so not removed.
Processing triggers for man-db ...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for desktop-file-utils ...
Processing triggers for gnome-menus ...
Processing triggers for hicolor-icon-theme ...
Processing triggers for install-info ...
christoph at christoph-Latitude-E4300:~$ R
The program 'R' is currently not installed. You can install it by typing:
sudo apt-get install r-base-core
christoph at christoph-Latitude-E4300:~$ sudo apt-get install r-base-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme
r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended
Suggested packages:
ess r-doc-info r-doc-pdf r-mathlib r-base-html texinfo texi2html
The following NEW packages will be installed
r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools
r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended
0 upgraded, 18 newly installed, 0 to remove and 20 not upgraded.
Need to get 0 B/35.6 MB of archives.
After this operation, 50.8 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
Selecting previously unselected package r-base-core.
(Reading database ... 427503 files and directories currently installed.)
Unpacking r-base-core (from .../r-base-core_3.0.1-3precise_amd64.deb) ...
Selecting previously unselected package r-base-dev.
Unpacking r-base-dev (from .../r-base-dev_3.0.1-3precise_all.deb) ...
Selecting previously unselected package r-cran-boot.
Unpacking r-cran-boot (from .../r-cran-boot_1.3-9-1precise0_all.deb) ...
Selecting previously unselected package r-cran-mass.
Unpacking r-cran-mass (from .../r-cran-mass_7.3-26-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-class.
Unpacking r-cran-class (from .../r-cran-class_7.3-7-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-cluster.
Unpacking r-cran-cluster (from .../r-cran-cluster_1.14.4-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-codetools.
Unpacking r-cran-codetools (from .../r-cran-codetools_0.2-8-2precise0_all.deb) ...
Selecting previously unselected package r-cran-foreign.
Unpacking r-cran-foreign (from .../r-cran-foreign_0.8.54-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-kernsmooth.
Unpacking r-cran-kernsmooth (from .../r-cran-kernsmooth_2.23-10-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-lattice.
Unpacking r-cran-lattice (from .../r-cran-lattice_0.20-15-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-matrix.
Unpacking r-cran-matrix (from .../r-cran-matrix_1.0-12-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-nlme.
Unpacking r-cran-nlme (from .../r-cran-nlme_3.1.109-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-mgcv.
Unpacking r-cran-mgcv (from .../r-cran-mgcv_1.7-23-1precise0_amd64.deb) ...
Selecting previously unselected package r-cran-nnet.
Unpacking r-cran-nnet (from .../r-cran-nnet_7.3-6-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-survival.
Unpacking r-cran-survival (from .../r-cran-survival_2.37-4-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-rpart.
Unpacking r-cran-rpart (from .../r-cran-rpart_4.1-1-2precise0_amd64.deb) ...
Selecting previously unselected package r-cran-spatial.
Unpacking r-cran-spatial (from .../r-cran-spatial_7.3-6-1precise0_amd64.deb) ...
Selecting previously unselected package r-recommended.
Unpacking r-recommended (from .../r-recommended_3.0.1-3precise_all.deb) ...
Processing triggers for install-info ...
Processing triggers for hicolor-icon-theme ...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf.index...
Processing triggers for desktop-file-utils ...
Processing triggers for gnome-menus ...
Processing triggers for man-db ...
Setting up r-base-core (3.0.1-3precise) ...
Creating config file /etc/R/Renviron with new version
mktexlsr: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
mktexlsr: Done.
Setting up r-base-dev (3.0.1-3precise) ...
Setting up r-cran-boot (1.3-9-1precise0) ...
Setting up r-cran-mass (7.3-26-1precise0) ...
Setting up r-cran-class (7.3-7-1precise0) ...
Setting up r-cran-cluster (1.14.4-1precise0) ...
Setting up r-cran-codetools (0.2-8-2precise0) ...
Setting up r-cran-foreign (0.8.54-1precise0) ...
Setting up r-cran-kernsmooth (2.23-10-2precise0) ...
Setting up r-cran-lattice (0.20-15-1precise0) ...
Setting up r-cran-matrix (1.0-12-1precise0) ...
Setting up r-cran-nlme (3.1.109-1precise0) ...
Setting up r-cran-mgcv (1.7-23-1precise0) ...
Setting up r-cran-nnet (7.3-6-2precise0) ...
Setting up r-cran-survival (2.37-4-2precise0) ...
Setting up r-cran-rpart (4.1-1-2precise0) ...
Setting up r-cran-spatial (7.3-6-1precise0) ...
Setting up r-recommended (3.0.1-3precise) ...
christoph at christoph-Latitude-E4300:~$
christoph at christoph-Latitude-E4300:~$ sudo R
R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> update.packages(checkBuilt=TRUE)
> update.packages(checkBuilt=TRUE)
Warning: package 'codetools' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'DBI' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'lattice' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'proxy' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'RColorBrewer' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'RMySQL' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'RSQLite' in library '/usr/lib/R/site-library' will not be updated
Warning: package 'bitops' in library '/usr/lib/R/library' will not be updated
Warning: package 'caTools' in library '/usr/lib/R/library' will not be updated
Warning: package 'DBI' in library '/usr/lib/R/library' will not be updated
Warning: package 'epiR' in library '/usr/lib/R/library' will not be updated
Warning: package 'gdata' in library '/usr/lib/R/library' will not be updated
Warning: package 'gtools' in library '/usr/lib/R/library' will not be updated
Warning: package 'proxy' in library '/usr/lib/R/library' will not be updated
Warning: package 'RColorBrewer' in library '/usr/lib/R/library' will not be updated
Warning: package 'RMySQL' in library '/usr/lib/R/library' will not be updated
Warning: package 'RSQLite' in library '/usr/lib/R/library' will not be updated
boot :
Version 1.3-7 installed in /usr/lib/R/site-library built under R 2.15.1
Version 1.3-9 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
class :
Version 7.3-5 installed in /usr/lib/R/site-library built under R 2.15.1
Version 7.3-7 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
cluster :
Version 1.14.3 installed in /usr/lib/R/site-library built under R 2.15.1
Version 1.14.4 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
epiR :
Version 0.9-48 installed in /usr/lib/R/site-library built under R 2.15.3
Version 0.9-48 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
foreign :
Version 0.8-53 installed in /usr/lib/R/site-library built under R 2.15.3
Version 0.8-54 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
KernSmooth :
Version 2.23-10 installed in /usr/lib/R/site-library built under R 2.15.3
Version 2.23-10 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
MASS :
Version 7.3-23 installed in /usr/lib/R/site-library built under R 2.15.2
Version 7.3-26 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
Matrix :
Version 1.0-11 installed in /usr/lib/R/site-library built under R 2.15.2
Version 1.0-12 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
mgcv :
Version 1.7-22 installed in /usr/lib/R/site-library built under R 2.15.1
Version 1.7-23 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
nlme :
Version 3.1-108 installed in /usr/lib/R/site-library built under R 2.15.2
Version 3.1-109 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
nnet :
Version 7.3-6 installed in /usr/lib/R/site-library built under R 2.15.3
Version 7.3-6 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
rpart :
Version 4.1-1 installed in /usr/lib/R/site-library built under R 2.15.3
Version 4.1-1 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
spatial :
Version 7.3-4 installed in /usr/lib/R/site-library built under R 2.15.1
Version 7.3-6 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
survival :
Version 2.36-14 installed in /usr/lib/R/site-library built under R 2.15.0
Version 2.37-4 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
gmodels :
Version 2.15.1 installed in /usr/lib/R/library built under R 2.12.1
Version 2.15.4 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
gplots :
Version 2.10.1 installed in /usr/lib/R/library built under R 2.13.1
Version 2.11.0.1 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
gregmisc :
Version 2.1.2 installed in /usr/lib/R/library built under R 2.14.1
Version 2.1.2 available at http://cran.stat.auckland.ac.nz
Update (y/N/c)? y
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/boot_1.3-9.tar.gz'
Content type 'application/x-gzip' length 231614 bytes (226 Kb)
opened URL
==================================================
downloaded 226 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/class_7.3-7.tar.gz'
Content type 'application/x-gzip' length 24692 bytes (24 Kb)
opened URL
==================================================
downloaded 24 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/cluster_1.14.4.tar.gz'
Content type 'application/x-gzip' length 253036 bytes (247 Kb)
opened URL
==================================================
downloaded 247 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/epiR_0.9-48.tar.gz'
Content type 'application/x-gzip' length 375546 bytes (366 Kb)
opened URL
==================================================
downloaded 366 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/foreign_0.8-54.tar.gz'
Content type 'application/x-gzip' length 320608 bytes (313 Kb)
opened URL
==================================================
downloaded 313 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/KernSmooth_2.23-10.tar.gz'
Content type 'application/x-gzip' length 33334 bytes (32 Kb)
opened URL
==================================================
downloaded 32 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/MASS_7.3-26.tar.gz'
Content type 'application/x-gzip' length 481973 bytes (470 Kb)
opened URL
==================================================
downloaded 470 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/Matrix_1.0-12.tar.gz'
Content type 'application/x-gzip' length 1649142 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/mgcv_1.7-23.tar.gz'
Content type 'application/x-gzip' length 531246 bytes (518 Kb)
opened URL
==================================================
downloaded 518 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/nlme_3.1-109.tar.gz'
Content type 'application/x-gzip' length 700708 bytes (684 Kb)
opened URL
==================================================
downloaded 684 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/nnet_7.3-6.tar.gz'
Content type 'application/x-gzip' length 29530 bytes (28 Kb)
opened URL
==================================================
downloaded 28 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/rpart_4.1-1.tar.gz'
Content type 'application/x-gzip' length 813735 bytes (794 Kb)
opened URL
==================================================
downloaded 794 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/spatial_7.3-6.tar.gz'
Content type 'application/x-gzip' length 44062 bytes (43 Kb)
opened URL
==================================================
downloaded 43 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/survival_2.37-4.tar.gz'
Content type 'application/x-gzip' length 1619938 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb
* installing *source* package ‘boot’ ...
** package ‘boot’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/boot’
* restoring previous ‘/usr/lib/R/site-library/boot’
* installing *source* package ‘cluster’ ...
** package ‘cluster’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c clara.c -o clara.o
gfortran -fpic -O3 -pipe -g -c daisy.f -o daisy.o
gfortran -fpic -O3 -pipe -g -c dysta.f -o dysta.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c fanny.c -o fanny.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gfortran -fpic -O3 -pipe -g -c mona.f -o mona.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pam.c -o pam.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sildist.c -o sildist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c spannel.c -o spannel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c twins.c -o twins.o
gcc -std=gnu99 -shared -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/cluster’
* restoring previous ‘/usr/lib/R/site-library/cluster’
* installing *source* package ‘foreign’ ...
** package ‘foreign’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c R_systat.c -o R_systat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c Rdbfread.c -o Rdbfread.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c Rdbfwrite.c -o Rdbfwrite.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c SASxport.c -o SASxport.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c avl.c -o avl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c dbfopen.c -o dbfopen.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c file-handle.c -o file-handle.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c format.c -o format.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c minitab.c -o minitab.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pfm-read.c -o pfm-read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sfm-read.c -o sfm-read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c spss.c -o spss.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c stataread.c -o stataread.o
gcc -std=gnu99 -shared -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/foreign/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/foreign’
* restoring previous ‘/usr/lib/R/site-library/foreign’
* installing *source* package ‘KernSmooth’ ...
** package ‘KernSmooth’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -O3 -pipe -g -c blkest.f -o blkest.o
gfortran -fpic -O3 -pipe -g -c cp.f -o cp.o
gfortran -fpic -O3 -pipe -g -c dgedi.f -o dgedi.o
gfortran -fpic -O3 -pipe -g -c dgefa.f -o dgefa.o
gfortran -fpic -O3 -pipe -g -c dgesl.f -o dgesl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gfortran -fpic -O3 -pipe -g -c linbin.f -o linbin.o
gfortran -fpic -O3 -pipe -g -c linbin2D.f -o linbin2D.o
gfortran -fpic -O3 -pipe -g -c locpoly.f -o locpoly.o
gfortran -fpic -O3 -pipe -g -c rlbin.f -o rlbin.o
gfortran -fpic -O3 -pipe -g -c sdiag.f -o sdiag.o
gfortran -fpic -O3 -pipe -g -c sstdiag.f -o sstdiag.o
gcc -std=gnu99 -shared -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/KernSmooth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/KernSmooth’
* restoring previous ‘/usr/lib/R/site-library/KernSmooth’
* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c MASS.c -o MASS.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c lqs.c -o lqs.o
gcc -std=gnu99 -shared -o MASS.so MASS.o lqs.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/MASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/MASS’
* restoring previous ‘/usr/lib/R/site-library/MASS’
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c CHMfactor.c -o CHMfactor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c Csparse.c -o Csparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c TMatrix_as.c -o TMatrix_as.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c Tsparse.c -o Tsparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c Mutils.c -o Mutils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c chm_common.c -o chm_common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c cs.c -o cs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c cs_utils.c -o cs_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dense.c -o dense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dgCMatrix.c -o dgCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dgTMatrix.c -o dgTMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dgeMatrix.c -o dgeMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dpoMatrix.c -o dpoMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dppMatrix.c -o dppMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dsCMatrix.c -o dsCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dsyMatrix.c -o dsyMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dspMatrix.c -o dspMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dtCMatrix.c -o dtCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dtTMatrix.c -o dtTMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dtrMatrix.c -o dtrMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c dtpMatrix.c -o dtpMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c factorizations.c -o factorizations.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c ldense.c -o ldense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c lgCMatrix.c -o lgCMatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c sparseQR.c -o sparseQR.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O3 -pipe -g -c abIndex.c -o abIndex.o
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[2]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD/Lib'
make[2]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD'
( cd Source ; make clean )
make[2]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD/Source'
make[2]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD/Source'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD'
( cd Source ; make clean )
make[2]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD/Source'
make[2]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD/Source'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/SuiteSparse_config'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/SuiteSparse_config'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD'
( cd Lib ; make )
make[2]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD/Lib'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_copy.c -o cholmod_copy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_dense.c -o cholmod_dense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Check/cholmod_check.c -o cholmod_check.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Check/cholmod_write.c -o cholmod_write.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Modify/cholmod_updown.c -o cholmod_updown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O3 -pipe -g -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o
make[2]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/CHOLMOD'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD'
( cd Source ; make lib )
make[2]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD/Source'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -c colamd_global.c -o colamd_global.o
colamd_global.c:22:44: warning: initialisation from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -c colamd.c -o colamd.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[2]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD/Source'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/COLAMD'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD'
( cd Source ; make lib )
make[2]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD/Source'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDINT -c amd_global.c -o amd_i_global.o
amd_global.c:81:41: warning: initialisation from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O3 -pipe -g -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
amd_global.c:81:41: warning: initialisation from incompatible pointer type [enabled by default]
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o
make[2]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD/Source'
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/AMD'
make[1]: Entering directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DNTIMER -fpic -O3 -pipe -g -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[1]: Leaving directory `/tmp/RtmpjDFbwj/R.INSTALL10e2fab8ff2/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/Matrix/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/Matrix’
* restoring previous ‘/usr/lib/R/site-library/Matrix’
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -O3 -pipe -g -c chol.f -o chol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c corStruct.c -o corStruct.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c gnls.c -o gnls.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c nlOptimizer.c -o nlOptimizer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c nlme.c -o nlme.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c nlmefit.c -o nlmefit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c nls.c -o nls.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fvisibility=hidden -fpic -O3 -pipe -g -c pdMat.c -o pdMat.o
gfortran -fpic -O3 -pipe -g -c rs.f -o rs.o
gcc -std=gnu99 -shared -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o rs.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/nlme’
* restoring previous ‘/usr/lib/R/site-library/nlme’
* installing *source* package ‘nnet’ ...
** package ‘nnet’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c nnet.c -o nnet.o
gcc -std=gnu99 -shared -o nnet.so nnet.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/nnet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/nnet’
* restoring previous ‘/usr/lib/R/site-library/nnet’
* installing *source* package ‘rpart’ ...
** package ‘rpart’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c anova.c -o anova.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c anovapred.c -o anovapred.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c branch.c -o branch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c bsplit.c -o bsplit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c choose_surg.c -o choose_surg.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c fix_cp.c -o fix_cp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c free_tree.c -o free_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c gini.c -o gini.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c graycode.c -o graycode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c insert_split.c -o insert_split.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c make_cp_list.c -o make_cp_list.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c make_cp_table.c -o make_cp_table.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c mysort.c -o mysort.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c nodesplit.c -o nodesplit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c partition.c -o partition.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c poisson.c -o poisson.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pred_rpart.c -o pred_rpart.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c print_tree.c -o print_tree.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rpart.c -o rpart.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rpart_callback.c -o rpart_callback.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rpartexp.c -o rpartexp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rpartexp2.c -o rpartexp2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rpcountup.c -o rpcountup.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rpmatrix.c -o rpmatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rundown.c -o rundown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c rundown2.c -o rundown2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c surrogate.c -o surrogate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c usersplit.c -o usersplit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c xpred.c -o xpred.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c xval.c -o xval.o
gcc -std=gnu99 -shared -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/rpart/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/rpart’
* restoring previous ‘/usr/lib/R/site-library/rpart’
* installing *source* package ‘spatial’ ...
** package ‘spatial’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c krc.c -o krc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pps.c -o pps.o
gcc -std=gnu99 -shared -o spatial.so init.o krc.o pps.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/spatial/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/spatial’
* restoring previous ‘/usr/lib/R/site-library/spatial’
* installing *source* package ‘survival’ ...
** package ‘survival’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agexact.c -o agexact.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agfit3.c -o agfit3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agfit5.c -o agfit5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agmart.c -o agmart.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agmart2.c -o agmart2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agscore.c -o agscore.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agsurv3.c -o agsurv3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agsurv4.c -o agsurv4.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c agsurv5.c -o agsurv5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c chinv2.c -o chinv2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c chinv3.c -o chinv3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c cholesky2.c -o cholesky2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c cholesky3.c -o cholesky3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c chsolve2.c -o chsolve2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c chsolve3.c -o chsolve3.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c concordance1.c -o concordance1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c cox_Rcallback.c -o cox_Rcallback.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxcount1.c -o coxcount1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxdetail.c -o coxdetail.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxexact.c -o coxexact.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxfit2.c -o coxfit2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxfit5.c -o coxfit5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxfit6.c -o coxfit6.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxmart.c -o coxmart.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxmart2.c -o coxmart2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxph_wtest.c -o coxph_wtest.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxsafe.c -o coxsafe.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxscho.c -o coxscho.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c coxscore.c -o coxscore.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c dmatrix.c -o dmatrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c doloop.c -o doloop.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c msurv.c -o msurv.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pyears1.c -o pyears1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pyears2.c -o pyears2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pyears3b.c -o pyears3b.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pystep.c -o pystep.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survConcordance.c -o survConcordance.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survdiff2.c -o survdiff2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survfit4.c -o survfit4.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survfitci.c -o survfitci.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survpenal.c -o survpenal.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survreg6.c -o survreg6.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survreg7.c -o survreg7.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survregc1.c -o survregc1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c survregc2.c -o survregc2.o
gcc -std=gnu99 -shared -o survival.so agexact.o agfit3.o agfit5.o agmart.o agmart2.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit2.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o init.o msurv.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/survival’
* restoring previous ‘/usr/lib/R/site-library/survival’
* installing *source* package ‘class’ ...
** package ‘class’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c class.c -o class.o
gcc -std=gnu99 -shared -o class.so class.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/class’
* restoring previous ‘/usr/lib/R/site-library/class’
* installing *source* package ‘epiR’ ...
** package ‘epiR’ successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
Error : package ‘survival’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘epiR’
* removing ‘/usr/lib/R/site-library/epiR’
* restoring previous ‘/usr/lib/R/site-library/epiR’
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c gdi.c -o gdi.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c magic.c -o magic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c mat.c -o mat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c matrix.c -o matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c mgcv.c -o mgcv.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c misc.c -o misc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c qp.c -o qp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c soap.c -o soap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c sparse-smooth.c -o sparse-smooth.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c tprs.c -o tprs.o
gcc -std=gnu99 -shared -o mgcv.so gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/lib/R/site-library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
* removing ‘/usr/lib/R/site-library/mgcv’
* restoring previous ‘/usr/lib/R/site-library/mgcv’
The downloaded source packages are in
‘/tmp/RtmpO2dLnD/downloaded_packages’
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/gmodels_2.15.4.tar.gz'
Content type 'application/x-gzip' length 38803 bytes (37 Kb)
opened URL
==================================================
downloaded 37 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/gplots_2.11.0.1.tar.gz'
Content type 'application/x-gzip' length 250489 bytes (244 Kb)
opened URL
==================================================
downloaded 244 Kb
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/gregmisc_2.1.2.tar.gz'
Content type 'application/x-gzip' length 13080 bytes (12 Kb)
opened URL
==================================================
downloaded 12 Kb
* installing *source* package ‘gmodels’ ...
** package ‘gmodels’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error : package ‘gdata’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘gmodels’
* removing ‘/usr/lib/R/library/gmodels’
* restoring previous ‘/usr/lib/R/library/gmodels’
* installing *source* package ‘gplots’ ...
** package ‘gplots’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Error : package ‘gtools’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘gplots’
* removing ‘/usr/lib/R/library/gplots’
* restoring previous ‘/usr/lib/R/library/gplots’
* installing *source* package ‘gregmisc’ ...
** package ‘gregmisc’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error : package ‘gdata’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘gregmisc’
* removing ‘/usr/lib/R/library/gregmisc’
* restoring previous ‘/usr/lib/R/library/gregmisc’
The downloaded source packages are in
‘/tmp/RtmpO2dLnD/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
There were 17 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘boot’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘cluster’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘foreign’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘KernSmooth’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘MASS’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘Matrix’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘nlme’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘nnet’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘rpart’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘spatial’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘survival’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘class’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘epiR’ had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘mgcv’ had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘gmodels’ had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘gplots’ had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘gregmisc’ had non-zero exit status
>
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