Question: Problem loading RdbiPgSQL
0
gravatar for Thomas Adams
12.4 years ago by
Thomas Adams60
Thomas Adams60 wrote:
I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have successfully built and installed (independently) versions 1.8 and 1.10 of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. However, when I attempt to load RdbiPgSQL, I get the following error: > library(RdbiPgSQL) Loading required package: Rdbi Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so' : /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: undefined symbol: PQfsize Error: package/namespace load failed for 'RdbiPgSQL' The library /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so does exist. Any suggestions? Regards, Tom -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
rdbi rdbipgsql • 530 views
ADD COMMENTlink modified 12.4 years ago by Seth Falcon7.4k • written 12.4 years ago by Thomas Adams60
Answer: Problem loading RdbiPgSQL
0
gravatar for Thomas Adams
12.4 years ago by
Thomas Adams60
Thomas Adams60 wrote:
I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have successfully built and installed (independently) versions 1.8 and 1.10 of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. However, when I attempt to load RdbiPgSQL, I get the following error: > library(RdbiPgSQL) Loading required package: Rdbi Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so' : /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: undefined symbol: PQfsize Error: package/namespace load failed for 'RdbiPgSQL' The library /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so does exist. Any suggestions? Regards, Tom -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
ADD COMMENTlink written 12.4 years ago by Thomas Adams60
Answer: Problem loading RdbiPgSQL
0
gravatar for Seth Falcon
12.4 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have > successfully built and installed (independently) versions 1.8 and 1.10 > of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. > However, when I attempt to load RdbiPgSQL, I get the following error: > > > library(RdbiPgSQL) > Loading required package: Rdbi > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.s o': > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: > undefined symbol: PQfsize > Error: package/namespace load failed for 'RdbiPgSQL' > > The library > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so > does exist. > > Any suggestions? Did you try using biocLite? Details in just about every other post on this list and on the BioC website. Anyhow, version 1.8.0 for Rdbi and RdbiPgSQL are the ones to use with R 2.4.1. What version of PostgreSQL are you using? We have tested against 8.1.4. If you have a different version, you might want to verify that PQfsize is indeed gone. I did: pg_config --version grep PQfsize `pg_config --includedir`/*.h + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.4 years ago by Seth Falcon7.4k
Seth, Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 installed and your grep command reveals that PQfsize is in the libpq-fe.h file located in /usr/include. In fact, when I install RdbiPgSQL from source, it's easy to see that the build process explicitly looks for the availability of libpq-fe.h. I do not have any control over what version of PostgreSQL we have installed, so migrating to version 8.1.4 (or whatever) is not possible at this time. Can anyone suggest an alternative way to install RdbiPgSQL that circumvents this problem? Is there a Linux binary available that I can install ? will this even work? Regards, Tom Seth Falcon wrote: > Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > > >> I am running R 2.4.1 (not Bioconductor) on a RedHat Linux system. I have >> successfully built and installed (independently) versions 1.8 and 1.10 >> of Rdbi and RdbiPgSQL. Rdbi loads without problems for both versions. >> However, when I attempt to load RdbiPgSQL, I get the following error: >> >> > library(RdbiPgSQL) >> Loading required package: Rdbi >> Error in dyn.load(x, as.logical(local), as.logical(now)) : >> unable to load shared library >> '/awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL. so': >> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so: >> undefined symbol: PQfsize >> Error: package/namespace load failed for 'RdbiPgSQL' >> >> The library >> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so >> does exist. >> >> Any suggestions? >> > > Did you try using biocLite? Details in just about every other > post on this list and on the BioC website. Anyhow, version 1.8.0 for > Rdbi and RdbiPgSQL are the ones to use with R 2.4.1. > > What version of PostgreSQL are you using? We have tested against > 8.1.4. If you have a different version, you might want to verify that > PQfsize is indeed gone. I did: > > pg_config --version > grep PQfsize `pg_config --includedir`/*.h > > + seth > > -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
ADD REPLYlink written 12.4 years ago by Thomas Adams60
Answer: Problem loading RdbiPgSQL
0
gravatar for Seth Falcon
12.4 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > Seth, > > Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 > installed and your grep command reveals that PQfsize is in the > libpq-fe.h file located in /usr/include. In fact, when I install > RdbiPgSQL from source, it's easy to see that the build process > explicitly looks for the availability of libpq-fe.h. That's good. I expect RdbiPgSQL will work with 7.4.8 (not sure, but I think your problem lies elsewhere). > I do not have any control over what version of PostgreSQL we have > installed, so migrating to version 8.1.4 (or whatever) is not possible > at this time. Can anyone suggest an alternative way to install > RdbiPgSQL that circumvents this problem? Is there a Linux binary > available that I can install ? will this even work? Did you try via biocLite? It might fail, but that failure might give us some clues. Can you look at the output of "ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so" both from the command line where you successfully built/installed RdbiPgSQL and from inside R using the system() command? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.4 years ago by Seth Falcon7.4k
Seth, Following your suggestion, I get: from a Linux prompt: ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so produces: libc.so.6 => /lib/tls/libc.so.6 (0x00329000) /lib/ld-linux.so.2 (0x00a17000) within R: > system("ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so") libc.so.6 => /lib/tls/libc.so.6 (0x0022d000) /lib/ld-linux.so.2 (0x00a17000) I'm guessing the "libc.so.6 =>?" line differences is suspicious? As far as trying installing via biocLite? I'm avoiding this route for the following reason: The system I am using, where R is installed and where I need it to work along with our PostgreSQL database, is in an isolated network without, direct access to the internet. So, the install process would be more complicated than using the biocLite install script, since I would have to individually download each package, use a two-step process to ftp the packages through a firewall, and install them (maybe you can suggest a simple way of doing this) separately. Also, it may be obvious, but I have to install R in a non-standard location due to our system restrictions. Thanks again for your help? Tom Seth Falcon wrote: > Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > > >> Seth, >> >> Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 >> installed and your grep command reveals that PQfsize is in the >> libpq-fe.h file located in /usr/include. In fact, when I install >> RdbiPgSQL from source, it's easy to see that the build process >> explicitly looks for the availability of libpq-fe.h. >> > > That's good. I expect RdbiPgSQL will work with 7.4.8 (not sure, but I > think your problem lies elsewhere). > > >> I do not have any control over what version of PostgreSQL we have >> installed, so migrating to version 8.1.4 (or whatever) is not possible >> at this time. Can anyone suggest an alternative way to install >> RdbiPgSQL that circumvents this problem? Is there a Linux binary >> available that I can install ? will this even work? >> > > Did you try via biocLite? It might fail, but that failure might give > us some clues. > > Can you look at the output of > > "ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so" > > both from the command line where you successfully built/installed > RdbiPgSQL and from inside R using the system() command? > > + seth > > -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
ADD REPLYlink written 12.4 years ago by Thomas Adams60
Hi Thomas, Why don't you show us the output of the compilation process? When you run R CMD check on the RdbiPgSQL source tarball that you used for installation, it creates an RdbiPgSQL.Rcheck folder with an 00install.out file inside. You could compare this 00install.out file with the output produced by our build system here http://bioconductor.org/checkResults/2.0/RdbiPgSQL/lamb1-checksrc.html (scroll down to the RdbiPgSQL.Rcheck/00install.out section) In particular pay attention to this line gcc -std=gnu99 -shared -L/usr/local/lib64 -o RdbiPgSQL.so PgSQL.o PgSQLInit.o -lpq ... For most R installations there will be no "-L/home/biocbuild/bbs-2.0-bioc/R/lib -lR" part like we have but this is OK (this only shows up if R itself has been initially configured with --enable-R-shlib at built time). Anyway, given that your resulting RdbiPgSQL.so file is not linked against the libpq library, I suspect something is going wrong with the above 'gcc -shared ...' command. Let's do some basic checking: 1) On a RPM-based system like yours (Red Hat), you must have the following RPMs installed: postgresql postgresql-devel postgresql-libs Check with 'rpm -qa | grep -i postgres' and send us the output if you have some doubts. 2) You should be able to compile and run this "hello world" program: #include <stdio.h> int main() { printf("hello world\n"); return 0; } Put this in test.c and compile with: gcc test.c -lpq You should be able to run it with ./a.out Now the -lpq option is not required here but it allows us to check that this executable has been properly linked to the libpq library (even if the test.c code doesn't use it). Check the links with hpages at wellington:~> ldd a.out linux-gate.so.1 => (0xffffe000) libpq.so.3 => /usr/lib/libpq.so.3 (0x40030000) libc.so.6 => /lib/tls/libc.so.6 (0x4004c000) libssl.so.0.9.7 => /usr/lib/libssl.so.0.9.7 (0x40162000) libcrypto.so.0.9.7 => /usr/lib/libcrypto.so.0.9.7 (0x40192000) libkrb5.so.17 => /usr/lib/libkrb5.so.17 (0x40283000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x402be000) libresolv.so.2 => /lib/libresolv.so.2 (0x402f0000) libnsl.so.1 => /lib/libnsl.so.1 (0x40304000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4031a000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) libdl.so.2 => /lib/libdl.so.2 (0x4032c000) libasn1.so.6 => /usr/lib/libasn1.so.6 (0x40330000) libroken.so.16 => /usr/lib/libroken.so.16 (0x40357000) libcom_err.so.2 => /lib/libcom_err.so.2 (0x40368000) libdb-4.2.so => /usr/lib/tls/libdb-4.2.so (0x4036b000) Yes there are a lot! But the most important is having this line libpq.so.3 => ... If you don't have this or if you were not able to compile test.c in the first place with an error like hpages at wellington:~> gcc test.c -lpq /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse- linux/bin/ld: cannot find -lpq collect2: ld returned 1 exit status then look at the 'gcc -shared ...' command in your RdbiPgSQL.Rcheck/00install.out file, look for the first -L option (could be -L/usr/lib, or -L/usr/local/lib, or -L/usr/local/lib64, etc...), make sure that there is a libpq.so.* file (or symlink) in the folder specified in this -L option and try to compile test.c again with this -L option i.e. with something like 'gcc test.c -L/usr/local/lib -lpq' (use _your_ -L option). It's important to put the -L option _before_ -lpq If this doesn't work or if you end up with an a.out executable that is not properly linked to libpq.so.3 (the trailing number 3 could be different for you) then you have a PostgreSQL or gcc installation/configuration problem and you will need to ask your local system administrator for help. Cheers, H. Thomas Adams wrote: > Seth, > > Following your suggestion, I get: > > from a Linux prompt: > > ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so > > produces: > > libc.so.6 => /lib/tls/libc.so.6 (0x00329000) > /lib/ld-linux.so.2 (0x00a17000) > > within R: > > > system("ldd > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so") > libc.so.6 => /lib/tls/libc.so.6 (0x0022d000) > /lib/ld-linux.so.2 (0x00a17000) > > I'm guessing the "libc.so.6 =>?" line differences is suspicious? > > As far as trying installing via biocLite? I'm avoiding this route for > the following reason: The system I am using, where R is installed and > where I need it to work along with our PostgreSQL database, is in an > isolated network without, direct access to the internet. So, the install > process would be more complicated than using the biocLite install > script, since I would have to individually download each package, use a > two-step process to ftp the packages through a firewall, and install > them (maybe you can suggest a simple way of doing this) separately. > > Also, it may be obvious, but I have to install R in a non-standard > location due to our system restrictions. > > Thanks again for your help? > > Tom > > > > Seth Falcon wrote: >> Thomas Adams <thomas.adams at="" noaa.gov=""> writes: >> >> >>> Seth, >>> >>> Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 >>> installed and your grep command reveals that PQfsize is in the >>> libpq-fe.h file located in /usr/include. In fact, when I install >>> RdbiPgSQL from source, it's easy to see that the build process >>> explicitly looks for the availability of libpq-fe.h. >>> >> That's good. I expect RdbiPgSQL will work with 7.4.8 (not sure, but I >> think your problem lies elsewhere). >> >> >>> I do not have any control over what version of PostgreSQL we have >>> installed, so migrating to version 8.1.4 (or whatever) is not possible >>> at this time. Can anyone suggest an alternative way to install >>> RdbiPgSQL that circumvents this problem? Is there a Linux binary >>> available that I can install ? will this even work? >>> >> Did you try via biocLite? It might fail, but that failure might give >> us some clues. >> >> Can you look at the output of >> >> "ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so" >> >> both from the command line where you successfully built/installed >> RdbiPgSQL and from inside R using the system() command? >> >> + seth >> >> > >
ADD REPLYlink written 12.4 years ago by Hervé Pagès ♦♦ 14k
Herve, Seth, & Sean, Thanks so much for your help. My problem with loading RdbiPgSQL is now resolved ? thank goodness! I am still not completely sure what the underlying cause of the problem was, but given with everything you had suggested and with what I had done, I *beleive* the problem was that RdbiPgSQL was not seeing the PostgreSQL libs due to PATH problems. What worked for me, was logging into the server where R is installed and, as superuser, installing RdbiPgSQL (after which, I changed permissions from root to my own). There may be PATH issues with my user ID (and with others on our system) which could also lead to conflicts, I suppose. Actually, I started having install issues with all R packages utilizing shared libraries when I started clean with the upgrade to R 2.5.0. So, that was a pretty clear indication that I was seeing a systematic problem? But all is resolved now and I can connect to our PostgreSQL databases without problems. BTW, now, when I use the ldd command, I get output much more like what you had showed me in your examples. Thanks again for your help! Regards, Tom Herve Pages wrote: > Hi Thomas, > > > Why don't you show us the output of the compilation process? When you run R CMD check on the > RdbiPgSQL source tarball that you used for installation, it creates an RdbiPgSQL.Rcheck folder > with an 00install.out file inside. You could compare this 00install.out file with the output > produced by our build system here > > http://bioconductor.org/checkResults/2.0/RdbiPgSQL/lamb1-checksrc.html > (scroll down to the RdbiPgSQL.Rcheck/00install.out section) > > In particular pay attention to this line > > gcc -std=gnu99 -shared -L/usr/local/lib64 -o RdbiPgSQL.so PgSQL.o PgSQLInit.o -lpq ... > > For most R installations there will be no "-L/home/biocbuild/bbs-2.0-bioc/R/lib -lR" part > like we have but this is OK (this only shows up if R itself has been initially configured > with --enable-R-shlib at built time). > Anyway, given that your resulting RdbiPgSQL.so file is not linked against the libpq > library, I suspect something is going wrong with the above 'gcc -shared ...' command. > > Let's do some basic checking: > > 1) On a RPM-based system like yours (Red Hat), you must have the following RPMs installed: > postgresql > postgresql-devel > postgresql-libs > Check with 'rpm -qa | grep -i postgres' and send us the output if you have some > doubts. > > 2) You should be able to compile and run this "hello world" program: > > #include <stdio.h> > int main() { > printf("hello world\n"); > return 0; > } > > Put this in test.c and compile with: > > gcc test.c -lpq > > You should be able to run it with ./a.out > Now the -lpq option is not required here but it allows us to check that this executable > has been properly linked to the libpq library (even if the test.c code doesn't use it). > Check the links with > > hpages at wellington:~> ldd a.out > linux-gate.so.1 => (0xffffe000) > libpq.so.3 => /usr/lib/libpq.so.3 (0x40030000) > libc.so.6 => /lib/tls/libc.so.6 (0x4004c000) > libssl.so.0.9.7 => /usr/lib/libssl.so.0.9.7 (0x40162000) > libcrypto.so.0.9.7 => /usr/lib/libcrypto.so.0.9.7 (0x40192000) > libkrb5.so.17 => /usr/lib/libkrb5.so.17 (0x40283000) > libcrypt.so.1 => /lib/libcrypt.so.1 (0x402be000) > libresolv.so.2 => /lib/libresolv.so.2 (0x402f0000) > libnsl.so.1 => /lib/libnsl.so.1 (0x40304000) > libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4031a000) > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > libdl.so.2 => /lib/libdl.so.2 (0x4032c000) > libasn1.so.6 => /usr/lib/libasn1.so.6 (0x40330000) > libroken.so.16 => /usr/lib/libroken.so.16 (0x40357000) > libcom_err.so.2 => /lib/libcom_err.so.2 (0x40368000) > libdb-4.2.so => /usr/lib/tls/libdb-4.2.so (0x4036b000) > > Yes there are a lot! But the most important is having this line > > libpq.so.3 => ... > > If you don't have this or if you were not able to compile test.c in the first place > with an error like > > hpages at wellington:~> gcc test.c -lpq > /usr/lib/gcc-lib/i586-suse-linux/3.3.4/../../../../i586-suse- linux/bin/ld: cannot find -lpq > collect2: ld returned 1 exit status > > then look at the 'gcc -shared ...' command in your RdbiPgSQL.Rcheck/00install.out file, > look for the first -L option (could be -L/usr/lib, or -L/usr/local/lib, > or -L/usr/local/lib64, etc...), make sure that there is a libpq.so.* file (or symlink) > in the folder specified in this -L option and try to compile test.c again with this -L option > i.e. with something like 'gcc test.c -L/usr/local/lib -lpq' (use _your_ -L option). > It's important to put the -L option _before_ -lpq > > If this doesn't work or if you end up with an a.out executable that is not properly > linked to libpq.so.3 (the trailing number 3 could be different for you) > then you have a PostgreSQL or gcc installation/configuration problem and you will > need to ask your local system administrator for help. > > > Cheers, > H. > > > Thomas Adams wrote: > >> Seth, >> >> Following your suggestion, I get: >> >> from a Linux prompt: >> >> ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so >> >> produces: >> >> libc.so.6 => /lib/tls/libc.so.6 (0x00329000) >> /lib/ld-linux.so.2 (0x00a17000) >> >> within R: >> >> > system("ldd >> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so") >> libc.so.6 => /lib/tls/libc.so.6 (0x0022d000) >> /lib/ld-linux.so.2 (0x00a17000) >> >> I'm guessing the "libc.so.6 =>?" line differences is suspicious? >> >> As far as trying installing via biocLite? I'm avoiding this route for >> the following reason: The system I am using, where R is installed and >> where I need it to work along with our PostgreSQL database, is in an >> isolated network without, direct access to the internet. So, the install >> process would be more complicated than using the biocLite install >> script, since I would have to individually download each package, use a >> two-step process to ftp the packages through a firewall, and install >> them (maybe you can suggest a simple way of doing this) separately. >> >> Also, it may be obvious, but I have to install R in a non-standard >> location due to our system restrictions. >> >> Thanks again for your help? >> >> Tom >> >> >> >> Seth Falcon wrote: >> >>> Thomas Adams <thomas.adams at="" noaa.gov=""> writes: >>> >>> >>> >>>> Seth, >>>> >>>> Thanks for your help and suggestions. Well, we have PostgreSQL 7.4.8 >>>> installed and your grep command reveals that PQfsize is in the >>>> libpq-fe.h file located in /usr/include. In fact, when I install >>>> RdbiPgSQL from source, it's easy to see that the build process >>>> explicitly looks for the availability of libpq-fe.h. >>>> >>>> >>> That's good. I expect RdbiPgSQL will work with 7.4.8 (not sure, but I >>> think your problem lies elsewhere). >>> >>> >>> >>>> I do not have any control over what version of PostgreSQL we have >>>> installed, so migrating to version 8.1.4 (or whatever) is not possible >>>> at this time. Can anyone suggest an alternative way to install >>>> RdbiPgSQL that circumvents this problem? Is there a Linux binary >>>> available that I can install ? will this even work? >>>> >>>> >>> Did you try via biocLite? It might fail, but that failure might give >>> us some clues. >>> >>> Can you look at the output of >>> >>> "ldd /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so" >>> >>> both from the command line where you successfully built/installed >>> RdbiPgSQL and from inside R using the system() command? >>> >>> + seth >>> >>> >>> >> > > > -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
ADD REPLYlink written 12.4 years ago by Thomas Adams60
Answer: Problem loading RdbiPgSQL
0
gravatar for Seth Falcon
12.4 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi Thomas, Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > Following your suggestion, I get: > > from a Linux prompt: > > ldd > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so > > produces: > > libc.so.6 => /lib/tls/libc.so.6 (0x00329000) > /lib/ld-linux.so.2 (0x00a17000) This is quite strange and very different from what I get on one of our Linux servers. ldd RLIBS/2.5/RdbiPgSQL/libs/RdbiPgSQL.so libpq.so.4 => /usr/lib64/libpq.so.4 (0x00002aaaaabd3000) libc.so.6 => /lib64/tls/libc.so.6 (0x00002aaaaacf5000) libssl.so.0.9.7 => /usr/lib64/libssl.so.0.9.7 (0x00002aaaaaf20000) libcrypto.so.0.9.7 => /usr/lib64/libcrypto.so.0.9.7 (0x00002aaaab057000) libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x00002aaaab28f000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00002aaaab407000) libresolv.so.2 => /lib64/libresolv.so.2 (0x00002aaaab541000) libnsl.so.1 => /lib64/libnsl.so.1 (0x00002aaaab655000) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x00002aaaab76b000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaab881000) libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x00002aaaab984000) libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00002aaaabaa8000) libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x00002aaaabbab000) In particular, the fact that your .so file doesn't link to libpq.so explains why you get the error message about PQfsize being missing. So now you need to figure out why you are ending up with an RdbiPgSQL.so that is not linked to libpq. You said that you found the PostgreSQL include files in /usr/include. Can you check that you also have libpq.so.* in /usr/lib? If so, have you tried: R CMD INSTALL \ --configure-args='--with-pgsql-libraries=/usr/lib --with-pgsql- libraries=/usr/include' \ RdbiPgSQL_1.8.0.tar.gz And capture all of the output in case this also does not work. > within R: > >> system("ldd > /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so") > libc.so.6 => /lib/tls/libc.so.6 (0x0022d000) > /lib/ld-linux.so.2 (0x00a17000) > > I'm guessing the "libc.so.6 =>?" line differences is suspicious? The only differences I see are the memory addresses and that is expected. > As far as trying installing via biocLite? I'm avoiding this route for > the following reason: The system I am using, where R is installed and > where I need it to work along with our PostgreSQL database, is in an > isolated network without, direct access to the internet. That's a good reason :-) -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.4 years ago by Seth Falcon7.4k
Seth Falcon wrote: > Hi Thomas, > > Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > >> Following your suggestion, I get: >> >> from a Linux prompt: >> >> ldd >> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so >> >> produces: >> >> libc.so.6 => /lib/tls/libc.so.6 (0x00329000) >> /lib/ld-linux.so.2 (0x00a17000) >> > > This is quite strange and very different from what I get on one of our > Linux servers. > > ldd RLIBS/2.5/RdbiPgSQL/libs/RdbiPgSQL.so > libpq.so.4 => /usr/lib64/libpq.so.4 (0x00002aaaaabd3000) > libc.so.6 => /lib64/tls/libc.so.6 (0x00002aaaaacf5000) > libssl.so.0.9.7 => /usr/lib64/libssl.so.0.9.7 (0x00002aaaaaf20000) > libcrypto.so.0.9.7 => /usr/lib64/libcrypto.so.0.9.7 (0x00002aaaab057000) > libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x00002aaaab28f000) > libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00002aaaab407000) > libresolv.so.2 => /lib64/libresolv.so.2 (0x00002aaaab541000) > libnsl.so.1 => /lib64/libnsl.so.1 (0x00002aaaab655000) > libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x00002aaaab76b000) > /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) > libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaab881000) > libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x00002aaaab984000) > libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00002aaaabaa8000) > libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x00002aaaabbab000) > > In particular, the fact that your .so file doesn't link to libpq.so > explains why you get the error message about PQfsize being missing. > So now you need to figure out why you are ending up with an > RdbiPgSQL.so that is not linked to libpq. > > You said that you found the PostgreSQL include files in /usr/include. > Can you check that you also have libpq.so.* in /usr/lib? If so, have > you tried: > > R CMD INSTALL \ > --configure-args='--with-pgsql-libraries=/usr/lib --with-pgsql- libraries=/usr/include' \ > RdbiPgSQL_1.8.0.tar.gz > And if that doesn't work, I would suggest installing postgresql from source into your home directory (or some other directory to which you have access) and try the same (with appropriate lib and include directories (note that the above should have --with-pgsql-includes=/usr/include, I think). We have not had trouble on either MacOS or linux with doing so. There is no need to run or even set up the installed version of postgresql, just link to its libraries. The compatibility between various versions of postgresql is pretty remarkable, so hopefully any newer version of postgresql will work for you. Sean
ADD REPLYlink written 12.4 years ago by Sean Davis21k
Sean & Seth, Thanks so much for your help and good suggestions. Unfortunately, none worked. I even went so far as to install R 2.5.0 and PostgreSQL 8.2.4 (into a local directory)? One interesting point, is that when I install RdbiPgSQL 1.8, the install script is still looking for the include file libpq-fe.h in /usr/include even though I have specified the PostgreSQL 8.2.4 libraries & includes elsewhere using: R CMD INSTALL \ --configure-args='--with-pgsql-libraries=/local-path/lib --with-pgsql- includes=/local-path/include' \ RdbiPgSQL_1.8.0.tar.gz xt4-tir:adams> b --with-pgsql-includes=/usr/include' RdbiPgSQL_1.8.0.tar.gz < Loading Tcl/Tk interface ... done * Installing to library '/awips/rep/lx/local_apps/R/lib/R/library' * Installing *source* package 'RdbiPgSQL' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for /usr/include/libpq-fe.h... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/awips/rep/lx/local_apps/R/lib/R/include -I/awips/rep/lx/local_apps/R/lib/R/include -I/awips/rep/lx/local_apps/proj4/include -I/usr/local/include -fpic -g -O2 -c PgSQL.c -o PgSQL.o gcc -std=gnu99 -I/awips/rep/lx/local_apps/R/lib/R/include -I/awips/rep/lx/local_apps/R/lib/R/include -I/awips/rep/lx/local_apps/proj4/include -I/usr/local/include -fpic -g -O2 -c PgSQLInit.c -o PgSQLInit.o gcc -std=gnu99 -shared -L/usr/local/lib -o RdbiPgSQL.so PgSQL.o PgSQLInit.o -L/awips/rep/lx/local_apps/proj4/lib ** R ** help >>> Building/Updating help pages for package 'RdbiPgSQL' Formats: text html latex example PgSQL text html latex dbAppendTable.PgSQL.conn text html latex dbClearResult.PgSQL.result text html latex dbColumnInfo.PgSQL.result text html latex dbConnect.PgSQL text html latex dbConnectionInfo.PgSQL.conn text html latex dbDisconnect.PgSQL.conn text html latex dbGetQuery.PgSQL.conn text html latex dbGetResult.PgSQL.result text html latex dbListTables.PgSQL.conn text html latex dbReadTable.PgSQL.conn text html latex dbResultInfo.PgSQL.result text html latex dbSendQuery.PgSQL.conn text html latex dbWriteTable.PgSQL.conn text html latex internal text html latex psql text html latex ** building package indices ... * DONE (RdbiPgSQL) This is getting very frustrating, because I do not have problems installing any other packages from source. Previously, about 1-year ago, I installed a package Rdbi.PgSQL, which worked fine with R 2.2.x. However, we have undergone a couple of Redhat system upgrades as well as going from IBM to (now) HP hardware, and a couple R updates. So, there are many confounding issues? Tom Sean Davis wrote: > Seth Falcon wrote: > >> Hi Thomas, >> >> Thomas Adams <thomas.adams at="" noaa.gov=""> writes: >> >> >>> Following your suggestion, I get: >>> >>> from a Linux prompt: >>> >>> ldd >>> /awips/rep/lx/local_apps/R/lib/R/library/RdbiPgSQL/libs/RdbiPgSQL.so >>> >>> produces: >>> >>> libc.so.6 => /lib/tls/libc.so.6 (0x00329000) >>> /lib/ld-linux.so.2 (0x00a17000) >>> >>> >> This is quite strange and very different from what I get on one of our >> Linux servers. >> >> ldd RLIBS/2.5/RdbiPgSQL/libs/RdbiPgSQL.so >> libpq.so.4 => /usr/lib64/libpq.so.4 (0x00002aaaaabd3000) >> libc.so.6 => /lib64/tls/libc.so.6 (0x00002aaaaacf5000) >> libssl.so.0.9.7 => /usr/lib64/libssl.so.0.9.7 (0x00002aaaaaf20000) >> libcrypto.so.0.9.7 => /usr/lib64/libcrypto.so.0.9.7 (0x00002aaaab057000) >> libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x00002aaaab28f000) >> libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00002aaaab407000) >> libresolv.so.2 => /lib64/libresolv.so.2 (0x00002aaaab541000) >> libnsl.so.1 => /lib64/libnsl.so.1 (0x00002aaaab655000) >> libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x00002aaaab76b000) >> /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) >> libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaab881000) >> libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x00002aaaab984000) >> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00002aaaabaa8000) >> libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x00002aaaabbab000) >> >> In particular, the fact that your .so file doesn't link to libpq.so >> explains why you get the error message about PQfsize being missing. >> So now you need to figure out why you are ending up with an >> RdbiPgSQL.so that is not linked to libpq. >> >> You said that you found the PostgreSQL include files in /usr/include. >> Can you check that you also have libpq.so.* in /usr/lib? If so, have >> you tried: >> >> R CMD INSTALL \ >> --configure-args='--with-pgsql-libraries=/usr/lib --with-pgsql- libraries=/usr/include' \ >> RdbiPgSQL_1.8.0.tar.gz >> >> > And if that doesn't work, I would suggest installing postgresql from > source into your home directory (or some other directory to which you > have access) and try the same (with appropriate lib and include > directories (note that the above should have > --with-pgsql-includes=/usr/include, I think). We have not had trouble > on either MacOS or linux with doing so. There is no need to run or even > set up the installed version of postgresql, just link to its libraries. > The compatibility between various versions of postgresql is pretty > remarkable, so hopefully any newer version of postgresql will work for you. > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: thomas.adams at noaa.gov VOICE: 937-383-0528 FAX: 937-383-0033
ADD REPLYlink written 12.4 years ago by Thomas Adams60
Answer: Problem loading RdbiPgSQL
0
gravatar for Seth Falcon
12.4 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Thomas Adams <thomas.adams at="" noaa.gov=""> writes: > Sean & Seth, > > Thanks so much for your help and good suggestions. Unfortunately, none > worked. I even went so far as to install R 2.5.0 and PostgreSQL 8.2.4 > (into a local directory)? > > One interesting point, is that when I install RdbiPgSQL 1.8, the > install script is still looking for the include file libpq-fe.h in > /usr/include even though I have specified the PostgreSQL 8.2.4 > libraries & includes elsewhere using: Another strange point is that somehow the install process doesn't seem to be linking against libpq. I'm baffled at the extent of your difficulties. I'm sure you are quite frustrated. It seems that you've been trying many things and I wonder if the state of the system is what you think it is. For example, did you edit the RdbiPgSQL package at any point? How many PostgreSQL installs do you have now? And so on. You need to figure out how to get RdbiPgSQL.so to link against libpq. This has to happen at compile time _and_ the libpq library needs to be resolvable at load time -- you may need to modify your LD_LIBRARY_PATH, for example, to get this to work. Good Luck. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.4 years ago by Seth Falcon7.4k
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