[R-sig-Geo] install of new maptools package fails
William McCoy
wdmccoy at geo.umass.edu
Tue Mar 22 17:06:31 CET 2011
I tried updating my installed packages on R today since the new rgeos
and maptools packages were out. The update of the maptools package
failed with the message:
> ERROR: installing package indices failed
I then tried removing the old maptools package and reinstalling it with
depend = TRUE to be sure I had all the needed dependencies. However it
still fails with:
> ** building package indices ...
> Warning: file 'gpcholes.rda' has magic number ''
> Use of save versions prior to 2 is deprecated
> Error : bad restore file magic number (file may be corrupted) -- no
data loaded
> ERROR: installing package indices failed
> * removing ‘/usr/share/R/library/maptools’
I'm not sure what the underlying cause is. Can someone suggest a solution?
The full text of the install.packages() output is below.
Bill
--
William D. McCoy
Geosciences
University of Massachusetts
Amherst, MA 01003
> install.packages("maptools", depend = TRUE, lib = "/usr/share/R/library")
trying URL
'http://software.rc.fas.harvard.edu/mirrors/R/src/contrib/maptools_0.8-3.tar.gz'
Content type 'application/x-gzip' length 894578 bytes (873 Kb)
opened URL
==================================================
downloaded 873 Kb
* installing *source* package ‘maptools’ ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rcentroid.c -o Rcentroid.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rgshhs.c -o Rgshhs.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rshapeget.c -o Rshapeget.o
Rshapeget.c: In function ‘Rshapeget’:
Rshapeget.c:24:32: warning: unused variable ‘nImpliedEOF’
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rshapeinfo.c -o
Rshapeinfo.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rshapewrite.c -o
Rshapewrite.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c Rshapewrite1.c -o
Rshapewrite1.o
Rshapewrite1.c: In function ‘shpwritepolys’:
Rshapewrite1.c:12:9: warning: ‘nShapeType’ may be used uninitialized in
this function
Rshapewrite1.c:15:29: warning: ‘padfZ’ may be used uninitialized in this
function
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c insiders.c -o insiders.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c pip.c -o pip.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c shpopen.c -o shpopen.o
shpopen.c:203:94: warning: ‘cvsid_aw’ defined but not used
shpopen.c: In function ‘SHPOpen’:
shpopen.c:507:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c shptree.c -o shptree.o
shptree.c:82:94: warning: ‘cvsid_aw’ defined but not used
shptree.c: In function ‘SHPWriteTree’:
shptree.c:969:11: warning: ignoring return value of ‘fwrite’, declared
with attribute warn_unused_result
shptree.c:971:11: warning: ignoring return value of ‘fwrite’, declared
with attribute warn_unused_result
shptree.c:975:11: warning: ignoring return value of ‘fwrite’, declared
with attribute warn_unused_result
shptree.c: In function ‘SHPWriteTreeNode’:
shptree.c:915:11: warning: ignoring return value of ‘fwrite’, declared
with attribute warn_unused_result
shptree.c: In function ‘SHPSearchDiskTree’:
shptree.c:829:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
shptree.c: In function ‘SHPSearchDiskTreeNode’:
shptree.c:731:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
shptree.c:734:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
shptree.c:735:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
shptree.c:744:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
shptree.c:771:14: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
shptree.c:786:10: warning: ignoring return value of ‘fread’, declared
with attribute warn_unused_result
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o maptools.so
Rcentroid.o Rgshhs.o Rshapeget.o Rshapeinfo.o Rshapewrite.o
Rshapewrite1.o insiders.o pip.o shpopen.o shptree.o -L/usr/lib64/R/lib -lR
installing to /usr/share/R/library/maptools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘maptools’
finding HTML links ... done
CCmaps html
Rd warning: /tmp/RtmpU9ikc7/R.INSTALL230eb10c/maptools/man/CCmaps.Rd:14:
missing file link ‘SpatialPolygonsDataFrame’
Rd warning: /tmp/RtmpU9ikc7/R.INSTALL230eb10c/maptools/man/CCmaps.Rd:33:
missing file link ‘SpatialPolygonsDataFrame’
ContourLines2SLDF html
GE_SpatialGrid html
Rgshhs html
Rd warning: /tmp/RtmpU9ikc7/R.INSTALL230eb10c/maptools/man/Rgshhs.Rd:31:
missing file link ‘gContainsProperly’
Rd warning: /tmp/RtmpU9ikc7/R.INSTALL230eb10c/maptools/man/Rgshhs.Rd:31:
missing file link ‘gContains’
SpatialLines2PolySet html
as.ppp html
asciigrid html
checkPolygonsHoles html
Rd warning:
/tmp/RtmpU9ikc7/R.INSTALL230eb10c/maptools/man/checkPolygonsHoles.Rd:20:
missing file link ‘gContainsProperly’
Rd warning:
/tmp/RtmpU9ikc7/R.INSTALL230eb10c/maptools/man/checkPolygonsHoles.Rd:20:
missing file link ‘gContains’
dotsInPolys html
elide-methods html
gcDestination html
getKMLcoordinates html
getinfo.shape html
gzAzimuth html
holepolys html
kmlLine html
kmlOverlay html
kmlPolygon html
leglabs html
map2SpatialPolygons html
nowrapRecenter html
pal2SpatialPolygons html
pointLabel html
ppp html
readGPS html
readShapeLines html
readShapePoints html
readShapePoly html
readShapeSpatial html
readSplus html
sp2Mondrian html
sp2WB html
sp2tmap html
spCbind-methods html
spRbind-methods html
sun-methods html
symbolsInPolys html
thinnedSpatialPoly html
unionSpatialPolygons html
wrld_simpl html
** building package indices ...
Warning: file 'gpcholes.rda' has magic number ''
Use of save versions prior to 2 is deprecated
Error : bad restore file magic number (file may be corrupted) -- no data
loaded
ERROR: installing package indices failed
* removing ‘/usr/share/R/library/maptools’
The downloaded packages are in
‘/tmp/Rtmp9LJc7G/downloaded_packages’
Warning message:
In install.packages("maptools", depend = TRUE, lib =
"/usr/share/R/library") :
installation of package 'maptools' had non-zero exit status
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