sp_0.9-16 source on CRAN
|
|
Roger Bivand
|
A new version of the foundation sp package is reaching CRAN mirrors, and
Windows and OSX binaries should follow within a day or so. There is a significant change in how SpatialGrid objects are created, which we hope will not affect users negatively, and which is giving a two orders of magnitude speedup for reading larger rasters (single band 900 by 3600 down from 12 minutes to 6 seconds on an older 1.5GHz machine). If anyone sees any negative impacts, please contact the authors immediately directly. Roger -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [hidden email] _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass Roger Bivand
Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway |
||||||||||||||||
Rainer M. Krug-3
|
Hi
I just upgraded to the new version, and I get an error message when importing an existing raster. The output is below. > readRAST6("Hakea_seeds_2007") Creating BIL support files ... Header File = ld World File = /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.wld Exporting Raster as double values(bytes=8) Using the Current Region settings ... north=6247000.000000 south=6195000.000000 east=270200.000000 west=251000.000000 r=520 c=192 Percent complete: r.out.bin complete. Error in readBinGrid(rtmpfl11, colname = vname[i], proj4string = p4, integer = to_int) : no such file: /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.hdr > The contents of the folder are as follow: (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux > ll Hakea* -rw-r--r-- 1 rkrug users 798720 2007-10-16 11:10 Hakea_seeds_2007 -rw-r--r-- 1 rkrug users 60 2007-10-16 11:10 Hakea_seeds_2007.wld -rw-r--r-- 1 rkrug users 798720 2007-10-16 10:52 Hakea_seedsDispersed_2007 -rw-r--r-- 1 rkrug users 60 2007-10-16 10:52 Hakea_seedsDispersed_2007.wld [Raster MASK present] GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux > Is there something wrong in my paths or os there a bug? Thanks a lot, Rainer Roger Bivand wrote: > A new version of the foundation sp package is reaching CRAN mirrors, and > Windows and OSX binaries should follow within a day or so. There is a > significant change in how SpatialGrid objects are created, which we hope > will not affect users negatively, and which is giving a two orders of > magnitude speedup for reading larger rasters (single band 900 by 3600 > down from 12 minutes to 6 seconds on an older 1.5GHz machine). > > If anyone sees any negative impacts, please contact the authors > immediately directly. > > Roger > _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
|
Roger Bivand
|
On Tue, 16 Oct 2007, Rainer M. Krug wrote:
> Hi > > I just upgraded to the new version, and I get an error message when importing > an existing raster. The output is below. This is not related to the sp update. Please do debug(readRAST6) and re-run, stepping through until you pass the the setting of the command string for r.out.bin. Please then print the cmd variable to screen and copy&paste it. It should have a -b flag. Please also give the output of sessionInfo() for your system, and the output of system("g.version") too. The *.wld file got put in the correct place, so the *.hdr ought to have been there too. If you do debug(readBinGrid), you'll see where it fails now, about 4 lines in. You could also do list.files(dirname(fname)) just before it fails in readBinGrid(), to check whether there ia anything else odd going on. Have you checked to see whether it has been written anywhere else? Roger > > >> readRAST6("Hakea_seeds_2007") > Creating BIL support files ... > Header File = ld > World File = > /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.wld > Exporting Raster as double values(bytes=8) > Using the Current Region settings ... > north=6247000.000000 > south=6195000.000000 > east=270200.000000 > west=251000.000000 > r=520 > c=192 > > Percent complete: > r.out.bin complete. > Error in readBinGrid(rtmpfl11, colname = vname[i], proj4string = p4, integer > = to_int) : > no such file: > /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.hdr >> > > The contents of the folder are as follow: > > (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >> ll Hakea* > -rw-r--r-- 1 rkrug users 798720 2007-10-16 11:10 Hakea_seeds_2007 > -rw-r--r-- 1 rkrug users 60 2007-10-16 11:10 Hakea_seeds_2007.wld > -rw-r--r-- 1 rkrug users 798720 2007-10-16 10:52 Hakea_seedsDispersed_2007 > -rw-r--r-- 1 rkrug users 60 2007-10-16 10:52 > Hakea_seedsDispersed_2007.wld > [Raster MASK present] > GRASS 6.2.2 > (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >> > > Is there something wrong in my paths or os there a bug? > > Thanks a lot, > > > Rainer > > > Roger Bivand wrote: >> A new version of the foundation sp package is reaching CRAN mirrors, and >> Windows and OSX binaries should follow within a day or so. There is a >> significant change in how SpatialGrid objects are created, which we hope >> will not affect users negatively, and which is giving a two orders of >> magnitude speedup for reading larger rasters (single band 900 by 3600 down >> from 12 minutes to 6 seconds on an older 1.5GHz machine). >> >> If anyone sees any negative impacts, please contact the authors >> immediately directly. >> >> Roger >> > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [hidden email] _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass Roger Bivand
Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway |
||||||||||||||||
|
Rainer M. Krug-3
|
Hi Roger
first of all thanks a lot for your prompt reply. I tried it with two other raster layers, and one worked. I played around, and the problem seems top be the length of the output variable: GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > r.out.bin -b input=Hakea_dc_2007 output=/home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee null=-1 Creating BIL support files ... Header File = eeeeee.wld <<<<<<------HERE IT IS NOT World File = /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld Exporting Raster as integer values (bytes=2) Using the Current Region settings ... north=6247000.000000 south=6195000.000000 east=270200.000000 west=251000.000000 r=520 c=192 Percent complete: 100% r.out.bin complete. [Raster MASK present] GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > ll /home/rkrug/eee* -rw-r--r-- 1 rkrug users 199680 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee -rw-r--r-- 1 rkrug users 60 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld [Raster MASK present] GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > r.out.bin -b input=Hakea_dc_2007 output=/home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee null=-1 Creating BIL support files ... Header File = /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.hdr <<<<<<------HERE IT IS World File = /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld Exporting Raster as integer values (bytes=2) Using the Current Region settings ... north=6247000.000000 south=6195000.000000 east=270200.000000 west=251000.000000 r=520 c=192 Percent complete: 100% r.out.bin complete. [Raster MASK present] GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > ll /home/rkrug/eee* -rw-r--r-- 1 rkrug users 199680 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee -rw-r--r-- 1 rkrug users 199680 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee -rw-r--r-- 1 rkrug users 60 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld -rw-r--r-- 1 rkrug users 83 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.hdr -rw-r--r-- 1 rkrug users 60 2007-10-16 12:18 /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld [Raster MASK present] GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > So it is a problem in grass itself. I should be able to find a way around, but I should file a bug report. Thanks a million, Rainer Roger Bivand wrote: > On Tue, 16 Oct 2007, Rainer M. Krug wrote: > >> Hi >> >> I just upgraded to the new version, and I get an error message when >> importing an existing raster. The output is below. > > This is not related to the sp update. Please do debug(readRAST6) and > re-run, stepping through until you pass the the setting of the command > string for r.out.bin. Please then print the cmd variable to screen and debug: tull <- ifelse(.Platform$OS.type == "windows", system(cmd), system(cmd, ignore.stderr = ignore.stderr)) Browse[1]> cmd [1] "r.out.bin -b input=Hakea_seeds_2007 output=/home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007 null=-1" Browse[1]> > copy&paste it. It should have a -b flag. Please also give the output of > sessionInfo() for your system, and the output of system("g.version") too. > sessionInfo() R version 2.6.0 (2007-10-03) i686-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] gstat_0.9-40 spgrass6_0.4-3 maptools_0.6-17 rgdal_0.5-15 [5] sp_0.9-16 foreign_0.8-23 loaded via a namespace (and not attached): [1] grid_2.6.0 lattice_0.16-5 > system("g.version") GRASS 6.2.2 (2007) > > > The *.wld file got put in the correct place, so the *.hdr ought to have > been there too. > > If you do debug(readBinGrid), you'll see where it fails now, about 4 > lines in. You could also do list.files(dirname(fname)) just before it > fails in readBinGrid(), to check whether there ia anything else odd > going on. Have you checked to see whether it has been written anywhere > else? > > Roger > >> >> >>> readRAST6("Hakea_seeds_2007") >> Creating BIL support files ... >> Header File = ld >> World File = >> /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.wld >> >> Exporting Raster as double values(bytes=8) >> Using the Current Region settings ... >> north=6247000.000000 >> south=6195000.000000 >> east=270200.000000 >> west=251000.000000 >> r=520 >> c=192 >> >> Percent complete: >> r.out.bin complete. >> Error in readBinGrid(rtmpfl11, colname = vname[i], proj4string = p4, >> integer = to_int) : >> no such file: >> /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.hdr >> >>> >> >> The contents of the folder are as follow: >> >> (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >> >>> ll Hakea* >> -rw-r--r-- 1 rkrug users 798720 2007-10-16 11:10 Hakea_seeds_2007 >> -rw-r--r-- 1 rkrug users 60 2007-10-16 11:10 Hakea_seeds_2007.wld >> -rw-r--r-- 1 rkrug users 798720 2007-10-16 10:52 >> Hakea_seedsDispersed_2007 >> -rw-r--r-- 1 rkrug users 60 2007-10-16 10:52 >> Hakea_seedsDispersed_2007.wld >> [Raster MASK present] >> GRASS 6.2.2 >> (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >> >>> >> >> Is there something wrong in my paths or os there a bug? >> >> Thanks a lot, >> >> >> Rainer >> >> >> Roger Bivand wrote: >>> A new version of the foundation sp package is reaching CRAN mirrors, >>> and >>> Windows and OSX binaries should follow within a day or so. There is a >>> significant change in how SpatialGrid objects are created, which we >>> hope >>> will not affect users negatively, and which is giving a two orders of >>> magnitude speedup for reading larger rasters (single band 900 by >>> 3600 down >>> from 12 minutes to 6 seconds on an older 1.5GHz machine). >>> >>> If anyone sees any negative impacts, please contact the authors >>> immediately directly. >>> >>> Roger >>> >> > _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
||||||||||||||||
|
Rainer M. Krug-3
|
In reply to this post
by Roger Bivand
Roger Bivand wrote:
> On Tue, 16 Oct 2007, Rainer M Krug wrote: > >> Hi Roger >> >> first of all thanks a lot for your prompt reply. I tried it with two >> other raster layers, and one worked. >> >> I played around, and the problem seems top be the length of the output >> variable: >> >> >> >> So it is a problem in grass itself. >> I should be able to find a way around, but I should file a bug report. > > Yes, I should have remembered that something like it did come up before. > I can see email traffic from July this year, thread here: > > http://grass.itc.it/pipermail/statsgrass/2007-July/000619.html > > So it is fixed in CVS for 6.3 and in CVS for 6.2.3. Thanks a lot for all your help - I'll work around the problem . And it is really MUCH faster now. Rainer > > Roger > >> >> Thanks a million, >> >> Rainer >> >> >> >> >> Roger Bivand wrote: >>> On Tue, 16 Oct 2007, Rainer M. Krug wrote: >>> >>> > Hi >>> > > I just upgraded to the new version, and I get an error message >>> when > importing an existing raster. The output is below. >>> >>> This is not related to the sp update. Please do debug(readRAST6) and >>> re-run, stepping through until you pass the the setting of the command >>> string for r.out.bin. Please then print the cmd variable to screen and >> >> debug: tull <- ifelse(.Platform$OS.type == "windows", system(cmd), >> system(cmd, >> ignore.stderr = ignore.stderr)) >> Browse[1]> cmd >> [1] "r.out.bin -b input=Hakea_seeds_2007 >> output=/home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007 >> null=-1" >> Browse[1]> >> >> >>> copy&paste it. It should have a -b flag. Please also give the output of >>> sessionInfo() for your system, and the output of system("g.version") >>> too. >> >>> sessionInfo() >> R version 2.6.0 (2007-10-03) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] gstat_0.9-40 spgrass6_0.4-3 maptools_0.6-17 rgdal_0.5-15 >> [5] sp_0.9-16 foreign_0.8-23 >> >> loaded via a namespace (and not attached): >> [1] grid_2.6.0 lattice_0.16-5 >> >> >>> system("g.version") >> GRASS 6.2.2 (2007) >>> >> >> >> >>> >>> The *.wld file got put in the correct place, so the *.hdr ought to have >>> been there too. >>> >>> If you do debug(readBinGrid), you'll see where it fails now, about 4 >>> lines >>> in. You could also do list.files(dirname(fname)) just before it >>> fails in >>> readBinGrid(), to check whether there ia anything else odd going on. >>> Have >>> you checked to see whether it has been written anywhere else? >>> >>> Roger >>> >>> > > > > readRAST6("Hakea_seeds_2007") >>> > Creating BIL support files ... >>> > Header File = ld >>> > World File = > >>> /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.wld >>> > > Exporting Raster as double values(bytes=8) >>> > Using the Current Region settings ... >>> > north=6247000.000000 >>> > south=6195000.000000 >>> > east=270200.000000 >>> > west=251000.000000 >>> > r=520 >>> > c=192 >>> > > Percent complete: >>> > r.out.bin complete. >>> > Error in readBinGrid(rtmpfl11, colname = vname[i], proj4string = >>> p4, > integer = to_int) : >>> > no such file: > >>> /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.hdr >>> > > > > > The contents of the folder are as follow: >>> > > >>> (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >>> > > > ll Hakea* >>> > -rw-r--r-- 1 rkrug users 798720 2007-10-16 11:10 Hakea_seeds_2007 >>> > -rw-r--r-- 1 rkrug users 60 2007-10-16 11:10 Hakea_seeds_2007.wld >>> > -rw-r--r-- 1 rkrug users 798720 2007-10-16 10:52 > >>> Hakea_seedsDispersed_2007 >>> > -rw-r--r-- 1 rkrug users 60 2007-10-16 10:52 > >>> Hakea_seedsDispersed_2007.wld >>> > [Raster MASK present] >>> > GRASS 6.2.2 > >>> (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >>> > > > > > Is there something wrong in my paths or os there a bug? >>> > > Thanks a lot, >>> > > > Rainer >>> > > > Roger Bivand wrote: >>> > > A new version of the foundation sp package is reaching CRAN >>> mirrors, > > and >>> > > Windows and OSX binaries should follow within a day or so. >>> There is a >>> > > significant change in how SpatialGrid objects are created, >>> which we > > hope >>> > > will not affect users negatively, and which is giving a two >>> orders of >>> > > magnitude speedup for reading larger rasters (single band 900 >>> by > > 3600 down >>> > > from 12 minutes to 6 seconds on an older 1.5GHz machine). >>> > > > > If anyone sees any negative impacts, please contact the >>> authors >>> > > immediately directly. >>> > > > > Roger >>> > > > >>> >> > _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
||||||||||||||||
|
Roger Bivand
|
In reply to this post
by Rainer M. Krug-3
On Tue, 16 Oct 2007, Rainer M Krug wrote:
> Hi Roger > > first of all thanks a lot for your prompt reply. I tried it with two other > raster layers, and one worked. > > I played around, and the problem seems top be the length of the output > variable: > > GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > r.out.bin -b > input=Hakea_dc_2007 > output=/home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee > null=-1 > Creating BIL support files ... > Header File = eeeeee.wld <<<<<<------HERE IT IS NOT > World File = > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld > Exporting Raster as integer values (bytes=2) > Using the Current Region settings ... > north=6247000.000000 > south=6195000.000000 > east=270200.000000 > west=251000.000000 > r=520 > c=192 > > Percent complete: 100% > r.out.bin complete. > [Raster MASK present] > GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > ll /home/rkrug/eee* > -rw-r--r-- 1 rkrug users 199680 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee > -rw-r--r-- 1 rkrug users 60 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld > [Raster MASK present] > GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > r.out.bin -b > input=Hakea_dc_2007 > output=/home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee > null=-1 > Creating BIL support files ... > Header File = > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.hdr > <<<<<<------HERE IT IS > World File = > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld > Exporting Raster as integer values (bytes=2) > Using the Current Region settings ... > north=6247000.000000 > south=6195000.000000 > east=270200.000000 > west=251000.000000 > r=520 > c=192 > > Percent complete: 100% > r.out.bin complete. > [Raster MASK present] > GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > ll /home/rkrug/eee* > -rw-r--r-- 1 rkrug users 199680 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee > -rw-r--r-- 1 rkrug users 199680 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee > -rw-r--r-- 1 rkrug users 60 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld > -rw-r--r-- 1 rkrug users 83 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.hdr > -rw-r--r-- 1 rkrug users 60 2007-10-16 12:18 > /home/rkrug/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee.wld > [Raster MASK present] > GRASS 6.2.2 (grass):~/Documents/Projects/AlienSpread/R > > > > So it is a problem in grass itself. > I should be able to find a way around, but I should file a bug report. Yes, I should have remembered that something like it did come up before. I can see email traffic from July this year, thread here: http://grass.itc.it/pipermail/statsgrass/2007-July/000619.html So it is fixed in CVS for 6.3 and in CVS for 6.2.3. Roger > > Thanks a million, > > Rainer > > > > > Roger Bivand wrote: >> On Tue, 16 Oct 2007, Rainer M. Krug wrote: >> >> > Hi >> > >> > I just upgraded to the new version, and I get an error message when >> > importing an existing raster. The output is below. >> >> This is not related to the sp update. Please do debug(readRAST6) and >> re-run, stepping through until you pass the the setting of the command >> string for r.out.bin. Please then print the cmd variable to screen and > > debug: tull <- ifelse(.Platform$OS.type == "windows", system(cmd), > system(cmd, > ignore.stderr = ignore.stderr)) > Browse[1]> cmd > [1] "r.out.bin -b input=Hakea_seeds_2007 > output=/home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007 > null=-1" > Browse[1]> > > >> copy&paste it. It should have a -b flag. Please also give the output of >> sessionInfo() for your system, and the output of system("g.version") too. > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] gstat_0.9-40 spgrass6_0.4-3 maptools_0.6-17 rgdal_0.5-15 > [5] sp_0.9-16 foreign_0.8-23 > > loaded via a namespace (and not attached): > [1] grid_2.6.0 lattice_0.16-5 > > >> system("g.version") > GRASS 6.2.2 (2007) >> > > > >> >> The *.wld file got put in the correct place, so the *.hdr ought to have >> been there too. >> >> If you do debug(readBinGrid), you'll see where it fails now, about 4 lines >> in. You could also do list.files(dirname(fname)) just before it fails in >> readBinGrid(), to check whether there ia anything else odd going on. Have >> you checked to see whether it has been written anywhere else? >> >> Roger >> >> > >> > >> > > readRAST6("Hakea_seeds_2007") >> > Creating BIL support files ... >> > Header File = ld >> > World File = >> > /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.wld >> > >> > Exporting Raster as double values(bytes=8) >> > Using the Current Region settings ... >> > north=6247000.000000 >> > south=6195000.000000 >> > east=270200.000000 >> > west=251000.000000 >> > r=520 >> > c=192 >> > >> > Percent complete: >> > r.out.bin complete. >> > Error in readBinGrid(rtmpfl11, colname = vname[i], proj4string = p4, >> > integer = to_int) : >> > no such file: >> > /home/rkrug/Documents/Projects/AlienSpread/R/../grass/simulation/.tmp/rkrug-linux/Hakea_seeds_2007.hdr >> > >> > > >> > >> > The contents of the folder are as follow: >> > >> > (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >> > >> > > ll Hakea* >> > -rw-r--r-- 1 rkrug users 798720 2007-10-16 11:10 Hakea_seeds_2007 >> > -rw-r--r-- 1 rkrug users 60 2007-10-16 11:10 Hakea_seeds_2007.wld >> > -rw-r--r-- 1 rkrug users 798720 2007-10-16 10:52 >> > Hakea_seedsDispersed_2007 >> > -rw-r--r-- 1 rkrug users 60 2007-10-16 10:52 >> > Hakea_seedsDispersed_2007.wld >> > [Raster MASK present] >> > GRASS 6.2.2 >> > (grass):~/Documents/Projects/AlienSpread/grass/simulation/.tmp/rkrug-linux >> > >> > > >> > >> > Is there something wrong in my paths or os there a bug? >> > >> > Thanks a lot, >> > >> > >> > Rainer >> > >> > >> > Roger Bivand wrote: >> > > A new version of the foundation sp package is reaching CRAN mirrors, >> > > and >> > > Windows and OSX binaries should follow within a day or so. There is a >> > > significant change in how SpatialGrid objects are created, which we >> > > hope >> > > will not affect users negatively, and which is giving a two orders of >> > > magnitude speedup for reading larger rasters (single band 900 by >> > > 3600 down >> > > from 12 minutes to 6 seconds on an older 1.5GHz machine). >> > > >> > > If anyone sees any negative impacts, please contact the authors >> > > immediately directly. >> > > >> > > Roger >> > > >> > >> > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [hidden email] _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass Roger Bivand
Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway |
||||||||||||||||
Markus Neteler-3
|
On Tue, Oct 16, 2007 at 12:49:57PM +0200, Roger Bivand wrote:
> On Tue, 16 Oct 2007, Rainer M Krug wrote: ... > > So it is a problem in grass itself. > > I should be able to find a way around, but I should file a bug report. > > Yes, I should have remembered that something like it did come up before. I > can see email traffic from July this year, thread here: > > http://grass.itc.it/pipermail/statsgrass/2007-July/000619.html > > So it is fixed in CVS for 6.3 and in CVS for 6.2.3. We should have 6.2.3 shortly (days), once Moritz has fixed another gis.m issue. Markus ------------------ ITC -> dall'1 marzo 2007 Fondazione Bruno Kessler ITC -> since 1 March 2007 Fondazione Bruno Kessler ------------------ _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
||||||||||||||||
Rainer M. Krug-2
|
Markus Neteler wrote:
> On Tue, Oct 16, 2007 at 12:49:57PM +0200, Roger Bivand wrote: >> On Tue, 16 Oct 2007, Rainer M Krug wrote: > ... >>> So it is a problem in grass itself. >>> I should be able to find a way around, but I should file a bug report. >> Yes, I should have remembered that something like it did come up before. I >> can see email traffic from July this year, thread here: >> >> http://grass.itc.it/pipermail/statsgrass/2007-July/000619.html >> >> So it is fixed in CVS for 6.3 and in CVS for 6.2.3. > > We should have 6.2.3 shortly (days), once Moritz has fixed > another gis.m issue. Good news Rainer > > Markus > > ------------------ > ITC -> dall'1 marzo 2007 Fondazione Bruno Kessler > ITC -> since 1 March 2007 Fondazione Bruno Kessler > ------------------ > > _______________________________________________ > statsgrass mailing list > [hidden email] > http://grass.itc.it/mailman/listinfo/statsgrass -- NEW EMAIL ADDRESS AND ADDRESS: [hidden email] [hidden email] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Plant Conservation Unit Department of Botany University of Cape Town Rondebosch 7701 South Africa Tel: +27 - (0)21 650 5776 (w) Fax: +27 - (0)86 516 2782 Fax: +27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [hidden email] [hidden email] _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
||||||||||||||||
Thomas Adams
|
In reply to this post
by Roger Bivand
Roger,
I am trying to compile spgrass6 on a Linux system with R 2.6.0. I have compiled all the dependencies without problems, but I am getting: xt4-tir:adams> R CMD INSTALL spgrass6_0.4-3.tar.gz * Installing to library '/awips/rep/lx/local_apps/R.dir/lib/R/library' * Installing *source* package 'spgrass6' ... ** R ** inst ** preparing package for lazy loading Loading required package: sp Loading required package: maptools Loading required package: foreign Loading required package: rgdal Error in dyn.load(file, ...) : unable to load shared library '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so': /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found (required by /usr/lib/libstdc++.so.6) Error: package 'rgdal' could not be loaded Execution halted ERROR: lazy loading failed for package 'spgrass6' ** Removing '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' ** Restoring previous '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' I don't understand this: /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found (required by /usr/lib/libstdc++.so.6) Do you have any insights? I have previously compiled spgrass6 without problems. But we have had some system changes since that time. System requirements force me to install in a non-standard location. Regards, Tom -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: [hidden email] VOICE: 937-383-0528 FAX: 937-383-0033 _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
||||||||||||||||
|
Roger Bivand
|
On Tue, 16 Oct 2007, Thomas Adams wrote:
> Roger, > > I am trying to compile spgrass6 on a Linux system with R 2.6.0. I have > compiled all the dependencies without problems, but I am getting: > > xt4-tir:adams> R CMD INSTALL spgrass6_0.4-3.tar.gz > * Installing to library '/awips/rep/lx/local_apps/R.dir/lib/R/library' > * Installing *source* package 'spgrass6' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: sp > Loading required package: maptools > Loading required package: foreign > Loading required package: rgdal > Error in dyn.load(file, ...) : > unable to load shared library > '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so': > /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found > (required by /usr/lib/libstdc++.so.6) > Error: package 'rgdal' could not be loaded > Execution halted > ERROR: lazy loading failed for package 'spgrass6' > ** Removing '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' > ** Restoring previous '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' > > I don't understand this: > > /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found > (required by /usr/lib/libstdc++.so.6) > > Do you have any insights? I have previously compiled spgrass6 without > problems. But we have had some system changes since that time. System > requirements force me to install in a non-standard location. What happens if you start R, say library(rgdal), and try to do - say - example(readGDAL)? If the same happens, then most likely rgdal was installed before the system upgrade, and you now have g++4, meaning that the dependencies of rgdal (or GDAL as a whole) are no longer met. If library(rgdal) fails as I suspect, you'll need to re-install it: install.packages("rgdal") ought to be enough, though GDAL may also need to be re-installed (all C++ programs are sensitive to build train upgrades, much more so than C programs). You may also do update.packages(checkBuilt=TRUE) which will freshen all the installed packages built with R < 2.6. If rgdal itself works, then sorry, no idea. Maybe somebody on the list (STATGRASS, R-sig-geo) may have seen something similar. How were R and GDAL installed, from source? What does g++ -v say? Roger > > Regards, > Tom > > > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [hidden email] _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass Roger Bivand
Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway |
||||||||||||||||
|
Thomas Adams
|
Roger,
Thank you very much for your suggestions. rgdal did fail to load into R. It turns out that the version of g++ is 3.4.4 implying some kind of mismatch between it and the shared library ../gcc_shlibs/libgcc_s.so.1, which I believe is unused anyhow. So, I simply moved it to another name. Can't see that that has caused any problems. Anyhow, I have re-compiled gdal, R 2.6.0, sp, and rgdal and now I am getting the following message, which is even more perplexing to me: > library(rgdal) Error in dyn.load(file, ...) : unable to load shared library '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so': /awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so: undefined symbol: OGR_G_GetY Error: package/namespace load failed for 'rgdal' which seems to imply (I think) that rgdal is not finding gdal when trying to load; is this correct? Regards, Tom Roger Bivand wrote: > On Tue, 16 Oct 2007, Thomas Adams wrote: > >> Roger, >> >> I am trying to compile spgrass6 on a Linux system with R 2.6.0. I >> have compiled all the dependencies without problems, but I am getting: >> >> xt4-tir:adams> R CMD INSTALL spgrass6_0.4-3.tar.gz >> * Installing to library '/awips/rep/lx/local_apps/R.dir/lib/R/library' >> * Installing *source* package 'spgrass6' ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Loading required package: sp >> Loading required package: maptools >> Loading required package: foreign >> Loading required package: rgdal >> Error in dyn.load(file, ...) : >> unable to load shared library >> '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so': >> /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found >> (required by /usr/lib/libstdc++.so.6) >> Error: package 'rgdal' could not be loaded >> Execution halted >> ERROR: lazy loading failed for package 'spgrass6' >> ** Removing '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' >> ** Restoring previous >> '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' >> >> I don't understand this: >> >> /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found >> (required by /usr/lib/libstdc++.so.6) >> >> Do you have any insights? I have previously compiled spgrass6 without >> problems. But we have had some system changes since that time. System >> requirements force me to install in a non-standard location. > > What happens if you start R, say library(rgdal), and try to do - say - > example(readGDAL)? If the same happens, then most likely rgdal was > installed before the system upgrade, and you now have g++4, meaning > that the dependencies of rgdal (or GDAL as a whole) are no longer met. > > If library(rgdal) fails as I suspect, you'll need to re-install it: > > install.packages("rgdal") > > ought to be enough, though GDAL may also need to be re-installed (all > C++ programs are sensitive to build train upgrades, much more so than > C programs). You may also do > > update.packages(checkBuilt=TRUE) > > which will freshen all the installed packages built with R < 2.6. > > If rgdal itself works, then sorry, no idea. Maybe somebody on the list > (STATGRASS, R-sig-geo) may have seen something similar. How were R and > GDAL installed, from source? What does g++ -v say? > > Roger > > >> >> Regards, >> Tom >> >> >> > -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: [hidden email] VOICE: 937-383-0528 FAX: 937-383-0033 _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass |
||||||||||||||||
|
Roger Bivand
|
On Wed, 17 Oct 2007, Thomas Adams wrote:
> Roger, > > Thank you very much for your suggestions. rgdal did fail to load into R. It > turns out that the version of g++ is 3.4.4 implying some kind of mismatch > between it and the shared library ../gcc_shlibs/libgcc_s.so.1, which I > believe is unused anyhow. So, I simply moved it to another name. Can't see > that that has caused any problems. > > Anyhow, I have re-compiled gdal, R 2.6.0, sp, and rgdal and now I am getting > the following message, which is even more perplexing to me: > >> library(rgdal) > Error in dyn.load(file, ...) : > unable to load shared library > '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so': > /awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so: undefined > symbol: OGR_G_GetY > Error: package/namespace load failed for 'rgdal' > > which seems to imply (I think) that rgdal is not finding gdal when trying to > load; is this correct? Well, it has found something, but it hasn't found at least one function inside that something. Are the ogr* utilities working from gdal directly, that is not using R? Does v.in.ogr in GRASS still work? Roger > > Regards, > Tom > > > Roger Bivand wrote: >> On Tue, 16 Oct 2007, Thomas Adams wrote: >> >> > Roger, >> > >> > I am trying to compile spgrass6 on a Linux system with R 2.6.0. I have >> > compiled all the dependencies without problems, but I am getting: >> > >> > xt4-tir:adams> R CMD INSTALL spgrass6_0.4-3.tar.gz >> > * Installing to library '/awips/rep/lx/local_apps/R.dir/lib/R/library' >> > * Installing *source* package 'spgrass6' ... >> > ** R >> > ** inst >> > ** preparing package for lazy loading >> > Loading required package: sp >> > Loading required package: maptools >> > Loading required package: foreign >> > Loading required package: rgdal >> > Error in dyn.load(file, ...) : >> > unable to load shared library >> > '/awips/rep/lx/local_apps/R.dir/lib/R/library/rgdal/libs/rgdal.so': >> > /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found >> > (required by /usr/lib/libstdc++.so.6) >> > Error: package 'rgdal' could not be loaded >> > Execution halted >> > ERROR: lazy loading failed for package 'spgrass6' >> > ** Removing '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' >> > ** Restoring previous >> > '/awips/rep/lx/local_apps/R.dir/lib/R/library/spgrass6' >> > >> > I don't understand this: >> > >> > /awips/hydro/lx/gcc_shlibs/libgcc_s.so.1: version `GCC_3.3' not found >> > (required by /usr/lib/libstdc++.so.6) >> > >> > Do you have any insights? I have previously compiled spgrass6 without >> > problems. But we have had some system changes since that time. System >> > requirements force me to install in a non-standard location. >> >> What happens if you start R, say library(rgdal), and try to do - say - >> example(readGDAL)? If the same happens, then most likely rgdal was >> installed before the system upgrade, and you now have g++4, meaning that >> the dependencies of rgdal (or GDAL as a whole) are no longer met. >> >> If library(rgdal) fails as I suspect, you'll need to re-install it: >> >> install.packages("rgdal") >> >> ought to be enough, though GDAL may also need to be re-installed (all C++ >> programs are sensitive to build train upgrades, much more so than C >> programs). You may also do >> >> update.packages(checkBuilt=TRUE) >> >> which will freshen all the installed packages built with R < 2.6. >> >> If rgdal itself works, then sorry, no idea. Maybe somebody on the list >> (STATGRASS, R-sig-geo) may have seen something similar. How were R and >> GDAL installed, from source? What does g++ -v say? >> >> Roger >> >> >> > >> > Regards, >> > Tom >> > >> > >> > >> > > > -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [hidden email] _______________________________________________ statsgrass mailing list [hidden email] http://grass.itc.it/mailman/listinfo/statsgrass Roger Bivand
Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway |
||||||||||||||||
| Free Embeddable Forum Powered by Nabble | Help |
