I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby gmake[3]: Entering directory `/l/fsc/dfs/src/R/src/library/eda' building package 'eda' ../../../library/eda/R/eda is unchanged ../../../library/eda/man/eda.Rd is unchanged /home/dfs/src/R/src/library/eda/src gmake[4]: Entering directory `/l/fsc/dfs/src/R/src/library/eda/src' config.status: error: invalid argument: src/library/eda/src/Makefile
building the development version
11 messages · Deborah Swayne, Brian Ripley, A.J. Rossini +2 more
Are you rebuilding?
./config.status
might need to be run to remake the Makefile, or:
./config.status --recheck ; ./config.status
(from top level directory in the R tree). I've had the same problems
before.
Deborah Swayne <dfs at research.att.com> writes:
I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby gmake[3]: Entering directory `/l/fsc/dfs/src/R/src/library/eda' building package 'eda' ../../../library/eda/R/eda is unchanged ../../../library/eda/man/eda.Rd is unchanged /home/dfs/src/R/src/library/eda/src gmake[4]: Entering directory `/l/fsc/dfs/src/R/src/library/eda/src' config.status: error: invalid argument: src/library/eda/src/Makefile
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rossini at u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
On Wed, 18 Feb 2004, Deborah Swayne wrote:
I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby
There should be no such directory. Did you do this in a clean build directory, as this is what would happen if you try to rebuild over sources from a couple of months ago? Please try again starting in an empty build directory.
gmake[3]: Entering directory `/l/fsc/dfs/src/R/src/library/eda' building package 'eda' ../../../library/eda/R/eda is unchanged ../../../library/eda/man/eda.Rd is unchanged /home/dfs/src/R/src/library/eda/src gmake[4]: Entering directory `/l/fsc/dfs/src/R/src/library/eda/src' config.status: error: invalid argument: src/library/eda/src/Makefile
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:
On Wed, 18 Feb 2004, Deborah Swayne wrote:
I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby
There should be no such directory. Did you do this in a clean build directory, as this is what would happen if you try to rebuild over sources from a couple of months ago? Please try again starting in an empty build directory.
This directory exists on a clean anonCVS checkout, cvs co, followed with a cvs update -Pd. Done AFTER Debbie's post, on a new machine. I verified Debbie's results, and the solution I suggested (2 incantations, with a weird incantation and the removal of the eda subdir) got me most of the way there. The second incantation was needed to cope with a problem in the ctest directory. best, -tony
rossini at u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
On Wed, 18 Feb 2004, A.J. Rossini wrote:
Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:
On Wed, 18 Feb 2004, Deborah Swayne wrote:
I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby
There should be no such directory. Did you do this in a clean build directory, as this is what would happen if you try to rebuild over sources from a couple of months ago? Please try again starting in an empty build directory.
This directory exists on a clean anonCVS checkout, cvs co, followed with a cvs update -Pd. Done AFTER Debbie's post, on a new machine.
Looks like there is a problem with anonCVS. That directory is empty in the master CVS tree and hence does not appear in the daily snapshots. I've just checked: it is not there in R-devel_2004-02-18.tar.bz2. What is in it under anonCVS?
I verified Debbie's results, and the solution I suggested (2 incantations, with a weird incantation and the removal of the eda subdir) got me most of the way there. The second incantation was needed to cope with a problem in the ctest directory.
Looks like we need to take some preventative measures in any case ....
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595
rossini at blindglobe.net (A.J. Rossini) writes:
Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:
On Wed, 18 Feb 2004, Deborah Swayne wrote:
I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby
There should be no such directory. Did you do this in a clean build directory, as this is what would happen if you try to rebuild over sources from a couple of months ago? Please try again starting in an empty build directory.
This directory exists on a clean anonCVS checkout, cvs co, followed with a cvs update -Pd. Done AFTER Debbie's post, on a new machine.
There should actually be an eda directory. On my system, with a fresh
checkout from the developer CVS, it ends up building a package
containing only
.noGenerics <- TRUE
.First.lib <- function(lib, pkg)
{
have.stats <- "package:stats" %in% search()
if(!have.stats) require("stats")
warning("package ", sQuote("eda"), " has been merged into ",
sQuote("stats"), call. = FALSE)
}
I can't reproduce Debbie's problem though...
O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
On 18 Feb 2004, Peter Dalgaard wrote:
rossini at blindglobe.net (A.J. Rossini) writes:
Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:
On Wed, 18 Feb 2004, Deborah Swayne wrote:
I'm trying to build the current development version of R on an SGI running IRIX6.5. Everything proceeds merrily until I reach the eda package. This is the error message I get if I cd to the appropriate directory and type 'make' or 'make all.' Does this make sense to anyone? -- Thanks, Debby
There should be no such directory. Did you do this in a clean build directory, as this is what would happen if you try to rebuild over sources from a couple of months ago? Please try again starting in an empty build directory.
This directory exists on a clean anonCVS checkout, cvs co, followed with a cvs update -Pd. Done AFTER Debbie's post, on a new machine.
There should actually be an eda directory. On my system, with a fresh
Yes, but no eda/src nor eda/man.
checkout from the developer CVS, it ends up building a package
containing only
.noGenerics <- TRUE
.First.lib <- function(lib, pkg)
{
have.stats <- "package:stats" %in% search()
if(!have.stats) require("stats")
warning("package ", sQuote("eda"), " has been merged into ",
sQuote("stats"), call. = FALSE)
}
I can't reproduce Debbie's problem though...
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:
On 18 Feb 2004, Peter Dalgaard wrote:
There should be no such directory. Did you do this in a clean build directory, as this is what would happen if you try to rebuild over sources from a couple of months ago? Please try again starting in an empty build directory.
This directory exists on a clean anonCVS checkout, cvs co, followed with a cvs update -Pd. Done AFTER Debbie's post, on a new machine.
There should actually be an eda directory. On my system, with a fresh
Yes, but no eda/src nor eda/man.
OK, that I can confirm. They do turn up on a checkout without the -P
option, but disappear after "cvs up -Pd". Tony, Debbie, did you
perhaps configure before attempting to prune the empty dirs? Could you
try
cvs -d ...blabla... co -P R
-p
BTW: Make dist appears to be broken?
O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Peter Dalgaard writes: > > OK, that I can confirm. They do turn up on a checkout without the -P > option, but disappear after "cvs up -Pd". Tony, Debbie, did you > perhaps configure before attempting to prune the empty dirs? Could you > try > > cvs -d ...blabla... co -P R I've use rsync; I don't know if that makes any difference: rsync -rC rsync.r-project.org::r-devel R In any case, I deleted all the old source code and started over, and the development version emerged without any difficulty. Thanks for helping me think about this. Debby
Deborah Swayne <dfs at research.att.com> writes:
Peter Dalgaard writes:
> > OK, that I can confirm. They do turn up on a checkout without the -P > option, but disappear after "cvs up -Pd". Tony, Debbie, did you > perhaps configure before attempting to prune the empty dirs? Could you > try > > cvs -d ...blabla... co -P R
I've use rsync; I don't know if that makes any difference: rsync -rC rsync.r-project.org::r-devel R
Hmm. It might mean that the rsync tree is built without the -P. If so, we should probably fix it.
In any case, I deleted all the old source code and started over, and the development version emerged without any difficulty.
Sounds like this was after Brian fixed the Makefiles.
O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Peter Dalgaard <p.dalgaard at biostat.ku.dk> writes:
Deborah Swayne <dfs at research.att.com> writes:
Peter Dalgaard writes:
> > OK, that I can confirm. They do turn up on a checkout without the -P > option, but disappear after "cvs up -Pd". Tony, Debbie, did you > perhaps configure before attempting to prune the empty dirs? Could you > try > > cvs -d ...blabla... co -P R
I've use rsync; I don't know if that makes any difference: rsync -rC rsync.r-project.org::r-devel R
Hmm. It might mean that the rsync tree is built without the -P. If so, we should probably fix it.
I think it is rather that Deborah's rsync call did not include a --delete option. The crontab entries that update the rsync trees all use -Pd (which I manage to remember because of your login). 11 * * * * (cd /spare1/R-src/r-patched; cvs -Q up -Pd -r R-1-8-patches; cd ../r-devel; cvs -Q up -Pd) 22 02 * * * (cd /spare1/ggobi-src/RSggobi; cvs -Q up -Pd; cd ../ggobi; cvs -Q up -Pd) 22 05 * * * (cd /spare1/R-project-web; cvs -Q up -Pd) 19 01 * * * (cd /spare1/Bioconductor-devel/madman; cvs -Q up -Pd)