R SIG Fedora - Nov 2011 - still working on building R from source

Hi Everyone: Gavin's been so generous and patient that I figured I'd
give
him a break and send this snag to the list. When I do get this working, I
will send  an "How to build R from the tarball " instructions message
to
this list for posterity's sake ( and myself and anyone else who doesn't
know how to build R from the tarball ).

So, here's my latest snag:  Gavin got me through the configure and the
make. So, then I did make check and I get below. But, since that error
didn't seem that serious, I figured I'd see whether R would run anyway.
The
output of the R command is below what's below. It's expecting a file in
/usr/lib/R I think ? But maybe the fact that the tests don't complete
successfully causes that. I looked to see if I have an ENVIRONMENT variable
for R in my
.bashrc but it doesn't have one. Thanks for all the help. From past
experiences, I knew it was going to be a long road and it has been but I'm
getting close.


Mark

END OF make check OUTPUT
#========================================================================================================make[2]:
Entering directory `/home/markleeds/R/2.14/build/tests'
running regression tests ...
make[3]: Entering directory `/home/markleeds/R/2.14/build/tests'
running code in '../../tests/reg-tests-1a.R' ... OK
running code in '../../tests/reg-tests-1b.R' ... OK
running code in '../../tests/reg-tests-2.R' ... OK
  comparing 'reg-tests-2.Rout' to
'../../tests/reg-tests-2.Rout.save' ... OK
running code in '../../tests/reg-examples1.R' ... OK
running code in '../../tests/reg-examples2.R' ... OK
running code in '../../tests/reg-packages.R' ...make[3]: ***
[reg-packages.Rout] Error 1
make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests'
make: *** [check] Error 2

# THEN TRY TO RUN R
#=================================================================================================
:~/R/2.14/build> R
/usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory
:~/R/2.14/build> ^C
:~/R/2.14/build>

	[[alternative HTML version deleted]]

i just realized that I had earlier instructions from marc schwartz, that
after I do the make check, to then log in as root and do make install. So,
I did that, logged out as root and typed R but still get the same message.
Below is some of the output from make install. There were no errors. Thanks.

make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/unix'
make[2]: Entering directory `/home/markleeds/R/2.14/build/src/main'
mkdir -p -- /usr/local/lib/R/bin/exec
make[3]: Entering directory `/home/markleeds/R/2.14/build/src/main'
make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/main'
make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/main'
make[2]: Entering directory `/home/markleeds/R/2.14/build/src/modules'
make[3]: Entering directory
`/home/markleeds/R/2.14/build/src/modules/internet'
mkdir -p -- /usr/local/lib/R/modules
make[3]: Leaving directory
`/home/markleeds/R/2.14/build/src/modules/internet'
make[3]: Entering directory
`/home/markleeds/R/2.14/build/src/modules/lapack'
make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/lapack'
make[3]: Entering directory
`/home/markleeds/R/2.14/build/src/modules/vfonts'
make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/vfonts'
make[3]: Entering directory `/home/markleeds/R/2.14/build/src/modules/X11'
make[3]: Leaving directory `/home/markleeds/R/2.14/build/src/modules/X11'
make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/modules'
make[2]: Entering directory `/home/markleeds/R/2.14/build/src/library'
mkdir -p -- /usr/local/lib/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory `/home/markleeds/R/2.14/build/src/library'
make[1]: Leaving directory `/home/markleeds/R/2.14/build/src'
make[1]: Entering directory `/home/markleeds/R/2.14/build/tests'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests'
make[1]: Entering directory `/home/markleeds/R/2.14/build/po'
installing translations:
mkdir -p -- /usr/local/lib/R/share/locale/en/LC_MESSAGES
  en
mkdir -p -- /usr/local/lib/R/share/locale/en_GB/LC_MESSAGES
  en_GB
mkdir -p -- /usr/local/lib/R/share/locale/es/LC_MESSAGES
  es
mkdir -p -- /usr/local/lib/R/share/locale/fr/LC_MESSAGES
  fr
mkdir -p -- /usr/local/lib/R/share/locale/de/LC_MESSAGES
  de
mkdir -p -- /usr/local/lib/R/share/locale/it/LC_MESSAGES
  it
mkdir -p -- /usr/local/lib/R/share/locale/ja/LC_MESSAGES
  ja
mkdir -p -- /usr/local/lib/R/share/locale/ko/LC_MESSAGES
  ko
mkdir -p -- /usr/local/lib/R/share/locale/nn/LC_MESSAGES
  nn
mkdir -p -- /usr/local/lib/R/share/locale/pt_BR/LC_MESSAGES
  pt_BR
mkdir -p -- /usr/local/lib/R/share/locale/ru/LC_MESSAGES
  ru
mkdir -p -- /usr/local/lib/R/share/locale/tr/LC_MESSAGES
  tr
mkdir -p -- /usr/local/lib/R/share/locale/zh_CN/LC_MESSAGES
  zh_CN
mkdir -p -- /usr/local/lib/R/share/locale/zh_TW/LC_MESSAGES
  zh_TW




On Sun, Nov 6, 2011 at 11:43 PM, Mark Leeds <markleeds2@gmail.com> wrote:
> Hi Everyone: Gavin's been so generous and patient that I figured
I'd give
> him a break and send this snag to the list. When I do get this working, I
> will send  an "How to build R from the tarball " instructions
message to
> this list for posterity's sake ( and myself and anyone else who
doesn't
> know how to build R from the tarball ).
>
> So, here's my latest snag:  Gavin got me through the configure and the
> make. So, then I did make check and I get below. But, since that error
> didn't seem that serious, I figured I'd see whether R would run
anyway. The
> output of the R command is below what's below. It's expecting a
file in
> /usr/lib/R I think ? But maybe the fact that the tests don't complete
> successfully causes that. I looked to see if I have an ENVIRONMENT variable
> for R in my
> .bashrc but it doesn't have one. Thanks for all the help. From past
> experiences, I knew it was going to be a long road and it has been but
I'm
> getting close.
>
>
> Mark
>
> END OF make check OUTPUT
>
>
#========================================================================================================>
make[2]: Entering directory `/home/markleeds/R/2.14/build/tests'
> running regression tests ...
> make[3]: Entering directory `/home/markleeds/R/2.14/build/tests'
> running code in '../../tests/reg-tests-1a.R' ... OK
> running code in '../../tests/reg-tests-1b.R' ... OK
> running code in '../../tests/reg-tests-2.R' ... OK
>   comparing 'reg-tests-2.Rout' to
'../../tests/reg-tests-2.Rout.save' ...
> OK
> running code in '../../tests/reg-examples1.R' ... OK
> running code in '../../tests/reg-examples2.R' ... OK
> running code in '../../tests/reg-packages.R' ...make[3]: ***
> [reg-packages.Rout] Error 1
> make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests'
> make[2]: *** [test-Reg] Error 2
> make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests'
> make[1]: *** [test-all-basics] Error 1
> make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests'
> make: *** [check] Error 2
>
> # THEN TRY TO RUN R
>
>
#=================================================================================================>
> :~/R/2.14/build> R
> /usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory
> :~/R/2.14/build> ^C
> :~/R/2.14/build>
>
>
	[[alternative HTML version deleted]]

On Sun, 2011-11-06 at 18:43 -0500, Mark Leeds wrote:
> Hi Everyone: Gavin's been so generous and patient that I figured
I'd give
> him a break and send this snag to the list. When I do get this working, I
> will send  an "How to build R from the tarball " instructions
message to
> this list for posterity's sake ( and myself and anyone else who
doesn't
> know how to build R from the tarball ).
I would question whether configure or make really did complete
correctly. Something went wrong if checking the compiled app failed.

You haven't shown us the conclusion of the configure step - it prints
out a list of capabilities and compilation options etc. Can you show
that. Also, can you show the configure arguments - i.e. how you called
configure?

Finally, can you show the last 10 or so lines of the output from make?

If you configured R as per my emails, you shouldn't need to go anywhere
near the root filesystem. I don't bother installing R I just run it from
the build DIR, which is in my ~/

I also build from svn which I find easier to maintain as I only need a

svn update path/to/sources

to get the latest patches.

You could also try again with a

make distclean

or

make clean

(I forget which is really required here) before you re-run configure,
just to make sure it has picked up the correct/new information.

HTH

G
> So, here's my latest snag:  Gavin got me through the configure and the
> make. So, then I did make check and I get below. But, since that error
> didn't seem that serious, I figured I'd see whether R would run
anyway. The
> output of the R command is below what's below. It's expecting a
file in
> /usr/lib/R I think ? But maybe the fact that the tests don't complete
> successfully causes that. I looked to see if I have an ENVIRONMENT variable
> for R in my
> .bashrc but it doesn't have one. Thanks for all the help. From past
> experiences, I knew it was going to be a long road and it has been but
I'm
> getting close.
> 
> 
> Mark
> 
> END OF make check OUTPUT
>
#========================================================================================================>
make[2]: Entering directory `/home/markleeds/R/2.14/build/tests'
> running regression tests ...
> make[3]: Entering directory `/home/markleeds/R/2.14/build/tests'
> running code in '../../tests/reg-tests-1a.R' ... OK
> running code in '../../tests/reg-tests-1b.R' ... OK
> running code in '../../tests/reg-tests-2.R' ... OK
>   comparing 'reg-tests-2.Rout' to
'../../tests/reg-tests-2.Rout.save' ... OK
> running code in '../../tests/reg-examples1.R' ... OK
> running code in '../../tests/reg-examples2.R' ... OK
> running code in '../../tests/reg-packages.R' ...make[3]: ***
> [reg-packages.Rout] Error 1
> make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests'
> make[2]: *** [test-Reg] Error 2
> make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests'
> make[1]: *** [test-all-basics] Error 1
> make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests'
> make: *** [check] Error 2
> 
> # THEN TRY TO RUN R
>
#=================================================================================================>
> :~/R/2.14/build> R
> /usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory
> :~/R/2.14/build> ^C
> :~/R/2.14/build>
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-SIG-Fedora mailing list
> R-SIG-Fedora at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> 
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