configure: error: libproj or sqlite3 not found in standard or given locations.

[pvo93]

I maintain ~1200 install and maintain R packages on a RHEL7 for which I don't have root access. I've found the best approach is to install all compiled libraries to support R packages in one place. I need to install sf as a dependency for other packages. I've successfully installed gdal, proj7, tiff-4, and geos. I've also installed a newer version of sqlite3 than what was on our system because one of these packages required it (proj7 I believe).

When I got the configure error "libproj or sqlite3 not found in standard or given locations," I initially thought it was because sqlite3 was not in a standard location because the sf config files don't use pkg-config for sqlite3 (although pkg-config is used for proj). However, when I execute the test on the command on the command line, I get the same error whether my PATH is pointing to the default sqlite3 install or mine. So, now I'm not sure if it's a sqlite3 issue at all.

[wa02042@mforgehn5 sf]$ ${CXX} ${CPPFLAGS} -o proj_conf_test proj_conf_test.cpp ${LIBS} -lsqlite3
/tmp/ccuBYW9n.o: In function main': proj_conf_test.cpp:(.text+0x5): undefined reference to proj_context_create'
collect2: error: ld returned 1 exit status
[wa02042@mforgehn5 sf]$ which sqlite3
/bin/sqlite3
[wa02042@mforgehn5 sf]$ sqlite3 --version
3.7.17 2013-05-20 00:56:22 118a3b35693b134d56ebd780123b7fd6f1497668

[wa02042@mforgehn4 sf]$ g++ -std=gnu++11 -I/usr/local/biotools/r/R-3.6.2/R-dependencies/include -o proj_conf_test proj_conf_test.cpp -lsqlite3
/tmp/ccnTaFWO.o: In function main': proj_conf_test.cpp:(.text+0x5): undefined reference to proj_context_create'
collect2: error: ld returned 1 exit status

[wa02042@mforgehn4 sf]$ rpm -E %{rhel}
7
[wa02042@mforgehn4 sf]$ which sqlite3
/usr/local/biotools/ver2/2.0.0/bin/sqlite3
[wa02042@mforgehn4 sf]$ sqlite3 --version
3.33.0 2020-08-14 13:23:32 fca8dc8b578f215a969cd899336378966156154710873e68b3d9ac5881b0ff3f
[wa02042@mforgehn4 sf]$ which g++
/usr/local/scl/devtoolset-8/root/usr/bin/g++
[wa02042@mforgehn4 sf]$ g++ --version
g++ (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I read through the other sqlite3 post where someone questioned if the -sqlite3 flag is necessary at all. I tried hacking the configure.ac file to skip over the test. I was able to get the shared library to compile, but there's a segfault when I try to load it into R.

[wa02042@mforgehn4 R]$ R --vanilla CMD INSTALL -l /usr/local/biotools/rpackages/R-3.6.2-latest sf

• installing source package â��sfâ�� ...
  files �configure�, �configure.ac� have the wrong MD5 checksums
  ** using staged installation
  configure: CC: gcc
  configure: CXX: g++ -std=gnu++11
  checking for gdal-config... /usr/local/biotools/ver2/2.0.0/bin/gdal-config
  checking gdal-config usability... yes
  configure: GDAL: 3.1.2
  checking GDAL version >= 2.0.1... yes
  checking for gcc... gcc
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether gcc accepts -g... yes
  checking for gcc option to accept ISO C89... none needed
  checking how to run the C preprocessor... gcc -E
  checking for grep that handles long lines and -e... /bin/grep
  checking for egrep... /bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking gdal.h usability... yes
  checking gdal.h presence... yes
  checking for gdal.h... yes
  checking GDAL: linking with --libs only... no
  checking GDAL: linking with --libs and --dep-libs... yes
  checking GDAL: /usr/local/biotools/ver2/2.0.0/share/gdal/pcs.csv readable... no
  checking GDAL: checking whether PROJ is available for linking:... yes
  checking GDAL: checking whether PROJ is available fur running:... yes
  configure: GDAL: 3.1.2
  configure: pkg-config proj exists, will use it
  configure: using proj.h.
  configure: PROJ: 7.1.0
  checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
  checking for geos-config... /usr/local/biotools/ver2/2.0.0/bin/geos-config
  checking geos-config usability... yes
  configure: GEOS: 3.8.1
  checking GEOS version >= 3.4.0... yes
  checking geos_c.h usability... yes
  checking geos_c.h presence... yes
  checking for geos_c.h... yes
  checking geos: linking with -L/usr/local/biotools/ver2/2.0.0/lib -lgeos_c... yes
  configure: Package CPP flags: -I/usr/local/biotools/ver2/2.0.0/include -DHAVE_PROJ_H -I/usr/local/biotools/ver2/2.0.0/include -I/usr/local/biotools/ver2/2.0.0/include
  configure: Package LIBS: -L/usr/local/biotools/ver2/2.0.0/lib -lproj -L/usr/local/biotools/ver2/2.0.0/lib -lgdal -lcrypto -lsqlite3 -lexpat -ljpeg -ltiff -lpng -L/usr/local/biotools/ver2/2.0.0/lib -lproj -lsqlite3 -lz -lpthread -lm -lrt -ldl -lpcre -lcurl -lxml2 -L/usr/local/biotools/ver2/2.0.0/lib -lgeos_c
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  make: Nothing to be done for 'all'.
  installing to /usr/local/biotools/rpackages/R-3.6.2-latest/00LOCK-sf/00new/sf/libs
  ** R
  ** demo
  ** inst
  ** byte-compile and prepare package for lazy loading
  in method for �dbWriteTable� with signature �"PostgreSQLConnection","character","sf"�: no definition for class �PostgreSQLConnection�
  in method for �dbDataType� with signature �"PostgreSQLConnection","sf"�: no definition for class �PostgreSQLConnection�
  in method for �coerce� with signature �"Spatial","sf"�: no definition for class �Spatial�
  in method for �coerce� with signature �"Spatial","sfc"�: no definition for class �Spatial�
  in method for �coerce� with signature �"sf","Spatial"�: no definition for class �Spatial�
  in method for �coerce� with signature �"sfc","Spatial"�: no definition for class �Spatial�
  in method for �coerce� with signature �"XY","Spatial"�: no definition for class �Spatial�
  in method for �coerce� with signature �"crs","CRS"�: no definition for class �CRS�
  ** help
  *** installing help indices
  *** copying figures
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  sh: line 1: 11870 Segmentation fault '/usr/local/biotools/r/R-3.6.2/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpBAXIVh/filed0442428581'

*** caught segfault ***
address 0x89156, cause 'memory not mapped'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: 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 sm <- strsplit(conditionMessage(e), "\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 && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
15: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
16: tools:::.test_load_package("sf", "/usr/local/biotools/rpackages/R-3.6.2-latest/00LOCK-sf/00new")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed

• removing '��/usr/local/biotools/rpackages/R-3.6.2-lates/sf'

Any feedback you could give me here would be greatly appreciated. Thank you.

[edzer]

sf doesn't need sqlite3 executable, but the sqlite3 library and header files. For fedora this is packaged in sqlite-devel.

The error you see is frequently seen when certain libraries on your system are installed at more than one place in different versions (e.g. packaged, as well as from source), see here.

[pvo93]

Thank you for the reply. I tried installing again using the --with-proj-lib flag and with --with-proj-include flags but got the same error. I find the message confusing because even though it says "libproj or sqlite3 not found in standard or given locations." I've found nothing in the documentation or configure files that let's specify the location of sqlite3. Is there an option to specify the location of the sqlite3 libraries?

I've verified that the proj lib is linked to my sqlite3 install. And, I compiled sf.so again with my hacked configure script without letting R test loading it. The resulting sf.so is linked to the proper proj and sqlite3 libs.

[wa02042@mforgehn4 R]$ ldd /usr/local/biotools/rpackages/R-3.6.2-latest/sf/libs/sf.so | grep proj
libproj.so.19 => /usr/local/biotools/ver2/2.0.0/lib/libproj.so.19 (0x00002ab53fc6d000)
[wa02042@mforgehn4 R]$ ls -l /usr/local/biotools/ver2/2.0.0/lib/libproj.so.19
lrwxrwxrwx 1 wa02042 r-installs 17 Aug 19 12:33 /usr/local/biotools/ver2/2.0.0/lib/libproj.so.19 -> libproj.so.19.1.0
[wa02042@mforgehn4 R]$ ldd /usr/local/biotools/rpackages/R-3.6.2-latest/sf/libs/sf.so | grep sql
libsqlite3.so.0 => /usr/local/biotools/ver2/2.0.0/lib/libsqlite3.so.0 (0x00002acaf5a22000)

This is not a standard Fedora box. It's a research node for the Mayo Clinic on which I don't have root access and can't use apt-get so I've compiled everything from source. Any further insight would be greatly appreciated.

[edzer]

I think the way forward is to stop breaking ./configure when this test breaks, maybe only giving a message that the test fails. It requires libsqlite3-dev, but that is not required if PROJ and GDAL were installed as binary packages.

[serbinsh]

I am having a similar problem

checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /data/software/gdal/3.1.2_hdf4/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 3.1.2
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 7.1.0
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
configure: error: libproj or sqlite3 not found in standard or given locations.
ERROR: configuration failed for package ‘sf’
* removing ‘/data/home/sserbin/R/library/sf’

The downloaded source packages are in
	‘/tmp/Rtmpq9oxYT/downloaded_packages’
Warning message:
In install.packages("sf", configure.args = c("--with-proj-include=/data/software/proj/7.1.0/include/",  :
  installation of package ‘sf’ had non-zero exit status
> q()

Is it possible to use a flag like --with-sqlite3-lib? like with proj? For reference here is what I tried

install.packages('sf', configure.args=c('--with-proj-include=/data/software/proj/7.1.0/include/','--with-proj-lib=/data/software/proj/7.1.0/lib/', '--with-proj=/data/software/proj/7.1.0') )

[edzer]

Feel free to submit a PR - I see this is a problem, someone has to solve it.

[grimli]

Hi,
I have had this problem too. I need to specify sqlite3 library paths because I can't install it on standard paths.
Specific parameters would be useful.

Anyway i managed this issue using environment vauables: LIBS, LDFLAGS, CPPFLAGS anc CFLAGS to specify non standard paths for the compiler.

Kind Regards

[rrobinson-RMS]

Hi What is the solution to this ? What env variables are you using for sql lite ?
I am have setup the following variable (to the correct file locations not list) for both sqlite3 and Proj7

LD_LIBRARY_PATH
LIBRARY_PATH
PATH
MANPATH
C_INCLUDE_PATH
CPLUS_INCLUDE_PAT
INCLUDE
PKG_CONFIG_PATH "
CMAKE_PREFIX_PATH

This is my error

checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... no
checking GDAL: linking with --libs and --dep-libs... yes
checking GDAL: /mnt/opt/Centos7/hpc/spack/spack_Oct_2020/opt/spack/linux-centos7-broadwell/gcc-7.3.1/gdal-3.2.0-7juusgnasjeppoqamonw253tvgpeaafs/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 3.2.0
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 7.1.0
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
configure: error: libproj or sqlite3 not found in standard or given locations.
ERROR: configuration failed for package ���sf���

removing ���/mnt/opt/Centos7/hpc/spack/spack_Oct_2020/opt/spack/linux-centos7-broadwell/gcc-7.3.1/r-4.0.3-tu34p762h7igt6pdf7wlfm4fnaxmxyne/rlib/R/library/sf���
The downloaded source packages are in
���/mnt/gpfs/tmp/R/RtmpDek6az/downloaded_packages���
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("sf") :
installation of package ���sf��� had non-zero exit status

[jekriske-lilly]

@rrobinson-RMS

I'm loading environment modules (lmod) within our ldpaths file within the R install to load sqlite and proj modules, both prepending PATH, CPATH, LD_LIBRARY_PATH, and PKG_CONFIG_PATH

[rrobinson-RMS]

Hi Jeff, Thanks for your answer I used to work at Lilly too some years ago !

I am using standard Linux environment modules ie module load ...
Then I after loading all modules just running R and installing from there.

the only variable you have listed above I am missing is CPATH.
Which I believe is the same as C_INCLUDE_PATH.
I've added it to my Proj + Sqlite modules.

but no still luck ! cheers

[jekriske-lilly]

Are you also loading the gdal module and can you confirm that both gdal and proj were compiled with the sqlite version you're using?

For proj, I'm using 7.2.0, but I forget the minimum version needed.

[rrobinson-RMS]

Fixed it, my GEOS module was not the one referenced in my GDAL module.

The Error message was completely unrelated unfortunately.

Thanks for your help jeff as mentioning GDAL made me start looking along the rest of the chain.

[ice4prince]

I have a similar problem. I'm thinking it is because I'm on the cluster and load the module for dgal, proj and geos sperately.
gdal/gcc/2.4.1
proj/gcc/6.0.0
geos/gcc/3.7.2

there is no version problems, but I got the same error with @serbinsh

• installing source package 'sf' ...
  ** using staged installation
  configure: CC: gcc
  configure: CXX: g++ -std=gnu++11
  checking for gdal-config... /cm/shared/apps/gdal/gcc/2.4.1/bin/gdal-config
  checking gdal-config usability... yes
  configure: GDAL: 2.4.1
  checking GDAL version >= 2.0.1... yes
  checking for gcc... gcc
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether gcc accepts -g... yes
  checking for gcc option to accept ISO C89... none needed
  checking how to run the C preprocessor... gcc -E
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking for egrep... /usr/bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking gdal.h usability... yes
  checking gdal.h presence... yes
  checking for gdal.h... yes
  checking GDAL: linking with --libs only... yes
  checking GDAL: /cm/shared/apps/gdal/gcc/2.4.1/share/gdal/pcs.csv readable... yes
  checking GDAL: checking whether PROJ is available for linking:... yes
  checking GDAL: checking whether PROJ is available fur running:... yes
  configure: GDAL: 2.4.1
  configure: pkg-config proj exists, will use it
  configure: using proj.h.
  configure: PROJ: 6.0.0
  checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
  configure: error: libproj or sqlite3 not found in standard or given locations.
  ERROR: configuration failed for package 'sf'
• removing '/home2/s205236/R/x86_64-pc-linux-gnu-library/4.0/sf'
  Warning message:
  In i.p(...) :
  installation of package '/tmp/RtmpDFwXL3/file1defe226a92cd/sf_1.0-0.tar.gz' had non-zero exit status

how shall I identify the directory for those modules and sqlite?

[ice4prince]

I am having a similar problem

checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /data/software/gdal/3.1.2_hdf4/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 3.1.2
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 7.1.0
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
configure: error: libproj or sqlite3 not found in standard or given locations.
ERROR: configuration failed for package ‘sf’
* removing ‘/data/home/sserbin/R/library/sf’

The downloaded source packages are in
	‘/tmp/Rtmpq9oxYT/downloaded_packages’
Warning message:
In install.packages("sf", configure.args = c("--with-proj-include=/data/software/proj/7.1.0/include/",  :
  installation of package ‘sf’ had non-zero exit status
> q()

Is it possible to use a flag like --with-sqlite3-lib? like with proj? For reference here is what I tried

install.packages('sf', configure.args=c('--with-proj-include=/data/software/proj/7.1.0/include/','--with-proj-lib=/data/software/proj/7.1.0/lib/', '--with-proj=/data/software/proj/7.1.0') )

I have the same issue. Have you succeeded? How did you find these directories?