问题
I'm trying to install Rgdal package, all packages and their dependancies I've installed them manuelly since my server is offline, I have struggled with those dependancies for a long time. but now I think I fix the problem, but my problem now I think has came from R, I cannot even figure out what's happen. this is the out put I gut when I run the commande install.packages("rgdal_1.2-15.tar.gz","/usr/lib64/R/library/",repos=NULL,configure.args="--with-proj-include=/usr/proj49/include/") on R:
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: CC: gcc -m64 -std=gnu99
configure: CXX: g++ -m64
configure: rgdal: 1.2-15
checking for /usr/bin/svnversion... no
configure: svn revision: 691
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.8.1
checking GDAL version >= 1.6.3... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
configure: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -I/usr/proj49/include/
checking proj_api.h presence and usability... yes
checking PROJ.4 version: ... > 4.8.0
/usr/bin/ld: warning: libproj.so.12, needed by /usr/lib64/libogdi.so.3, may conflict with libproj.so.0
./configure: line 2112: 27095 Segmentation fault (core dumped) ./proj_conf_test2
checking PROJ.4: epsg found and readable... yes
/usr/bin/ld: warning: libproj.so.12, needed by /usr/lib64/libogdi.so.3, may conflict with libproj.so.0
./configure: line 2187: 27107 Segmentation fault (core dumped) ./proj_conf_test3
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags: -I/usr/include/gdal -I/usr/proj49/include/
configure: Package LIBS: -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c init.c -o init.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c inverser.c -o inverser.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c local_stubs.c -o local_stubs.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_geom.cpp -o ogr_geom.o
ogr_geom.cpp: In function ‘SEXPREC* R_OGR_CAPI_features(SEXPREC*, SEXPREC*, SEXPREC*)’:
ogr_geom.cpp:39: warning: ‘mp_count_k0’ may be used uninitialized in this function
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c ogr_polygons.c -o ogr_polygons.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_proj.cpp -o ogr_proj.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogrdrivers.cpp -o ogrdrivers.o
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ogrsource.cpp -o ogrsource.o
ogrsource.cpp: In function ‘SEXPREC* ogrReadListColumn(OGRLayer*, SEXPREC*, int, int, int)’:
ogrsource.cpp:651: warning: unused variable ‘DINT_MAX’
ogrsource.cpp:652: warning: unused variable ‘DINT_MIN’
g++ -m64 -std=c++0x -I/usr/include/R -DNDEBUG -I/usr/include/gdal -I/usr/proj49/include/ -I/usr/local/include -I"/usr/lib64/R/library/sp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c projectit.cpp -o projectit.o
g++ -m64 -std=c++0x -shared -L/usr/lib64/R/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -lgdal -lproj -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/rgdal/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘rgdal’
finding HTML links ... done
CRS-class html
GDALDataset-class html
GDALDriver-class html
GDALMajorObject-class html
GDALRasterBand-class html
GDALReadOnlyDataset-class html
GDALReadOnlyDataset-methods html
GDALTransientDataset-class html
GridsDatums html
RGB2PCT html
SGDF2PCT html
SpatialGDAL-class html
closeDataset-methods html
displayDataset html
llgrid html
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/llgrid.Rd:11: missing file link ‘Spatial’
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/llgrid.Rd:16: missing file link ‘gridat’
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/llgrid.Rd:17: missing file link ‘gridat’
make_EPSG html
nor2k html
projInfo html
project html
readGDAL html
Rd warning: /tmp/RtmpKNPZgP/R.INSTALL68d7595014d0/rgdal/man/readGDAL.Rd:136: missing file link ‘flipVertical’
readOGR html
showWKT html
spTransform-methods html
wrappers html
writeOGR html
** building package indices
** installing vignettes
** testing if installed package can be loaded
sh: line 1: 28842 Segmentation fault (core dumped) '/usr/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpKNPZgP/file68d75bc50ad1'
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Traceback:
1: .Call("PROJ4_proj_def_dat_Installed", PACKAGE = "rgdal")
2: assign("has_proj_def.dat", .Call("PROJ4_proj_def_dat_Installed", PACKAGE = "rgdal"), envir = .RGDAL_CACHE)
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
14: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)})
15: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
16: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
17: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
22: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
23: tools:::.test_load_package("rgdal", "/usr/lib64/R/library")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing ‘/usr/lib64/R/library/rgdal’
Warning message:
In install.packages("rgdal_1.2-15.tar.gz", "/usr/lib64/R/library/", :
installation of package ‘rgdal_1.2-15.tar.gz’ had non-zero exit status
Update:
even with a newer version of Rgdal install.packages("rgdal_1.2-18.tar.gz","/usr/lib64/R/library/",repos=NULL,configure.args="--with-proj-include=/usr/proj49/include/"), I got the same error
来源：https://stackoverflow.com/questions/50064673/cannot-install-rgdal-package-in-local-server-an-irrecoverable-exception-occurre