Hi everyone,
My name is Anguel and I am new to this list.
1. I am trying to implement some simple example of a C++ compiled function from Hadley Wickham's website (http://adv-r.had.co.nz/Rcpp.html#rcpp).
In fact the function I am trying to compile is the first one:
library(Rcpp)
cppFunction('int add(int x, int y, int z) {
int sum = x + y + z;
return sum;
}')
2. Unfortunately I have immediately run into a problem, getting an error message:
Error in dyn.load("/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so") :
unable to load shared object '/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so':
dlopen(/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so, 6): Symbol not found: ___addtf3
Referenced from: /usr/local/lib/libquadmath.0.dylib
Expected in: /usr/local/lib/libgcc_s.1.dylib
in /usr/local/lib/libquadmath.0.dylib
3. I am working on OS X Maverics (10.9.3) and I am using R3.2.0
platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major 3
minor 2.0
year 2015
month 04
day 16
svn rev 68180
language R
version.string R version 3.2.0 (2015-04-16)
nickname Full of Ingredients
4. I'm also using RcppArmadillo_0.6.500.4.0 and
Rcpp_0.12.3
5. I can't seem to find any suggestions on the Internet concerning such a problem (maybe somebody will direct me in this regard).
6. I'll be extremely thankful to everybody who can direct me as to how to proceed from here. Of course, I'll be glad to provide any other information should you decide to answer my e-mail and request it.
Thank you in advance.
Anguel
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20160204/7f5c2318/attachment.html>
[Rcpp-devel] Rcpp problem related to sourceCpp_1.so
6 messages · Balamuta, James Joseph, Dirk Eddelbuettel, aakremena at aol.com
Greetings and Salutations, See: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/ Also, another example / more help setting up the dev environment on OS X is here: http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/ Happy Rcppin? Sincerely, JJB From: <rcpp-devel-bounces at lists.r-forge.r-project.org<mailto:rcpp-devel-bounces at lists.r-forge.r-project.org>> on behalf of "aakremena at aol.com<mailto:aakremena at aol.com>" <aakremena at aol.com<mailto:aakremena at aol.com>> Date: Thursday, February 4, 2016 at 4:57 PM To: "rcpp-devel at lists.r-forge.r-project.org<mailto:rcpp-devel at lists.r-forge.r-project.org>" <rcpp-devel at lists.r-forge.r-project.org<mailto:rcpp-devel at lists.r-forge.r-project.org>> Subject: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so Hi everyone, My name is Anguel and I am new to this list. 1. I am trying to implement some simple example of a C++ compiled function from Hadley Wickham's website (http://adv-r.had.co.nz/Rcpp.html#rcpp<https://urldefense.proofpoint.com/v2/url?u=http-3A__adv-2Dr.had.co.nz_Rcpp.html-23rcpp&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=Oj62bnDE1oueLU-seL9f0p1xxu4Hvw2JDuP8BUw91c8&m=WvdoHrvW5pvxSB9ksFcsptZw8fIa15tgk2vm6l-q3Sw&s=kpSJ5RNEN4SuABscb89E5CtCbR_XykCZ9MPBsGU6yBI&e=>). In fact the function I am trying to compile is the first one: library(Rcpp) cppFunction('int add(int x, int y, int z) { int sum = x + y + z; return sum;}') 2. Unfortunately I have immediately run into a problem, getting an error message: Error in dyn.load("/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so") : unable to load shared object '/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so': dlopen(/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib in /usr/local/lib/libquadmath.0.dylib 3. I am working on OS X Maverics (10.9.3) and I am using R3.2.0 platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 2.0 year 2015 month 04 day 16 svn rev 68180 language R version.string R version 3.2.0 (2015-04-16) nickname Full of Ingredients 4. I'm also using RcppArmadillo_0.6.500.4.0 and Rcpp_0.12.3 5. I can't seem to find any suggestions on the Internet concerning such a problem (maybe somebody will direct me in this regard). 6. I'll be extremely thankful to everybody who can direct me as to how to proceed from here. Of course, I'll be glad to provide any other information should you decide to answer my e-mail and request it. Thank you in advance. Anguel -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20160204/2f53aaca/attachment.html>
Hi James, Thank you so much. Anguel -----Original Message----- From: Balamuta, James Joseph <balamut2 at illinois.edu> To: aakremena <aakremena at aol.com>; rcpp-devel <rcpp-devel at lists.r-forge.r-project.org> Sent: Thu, Feb 4, 2016 5:58 pm Subject: Re: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so Greetings and Salutations, See: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/ Also, another example / more help setting up the dev environment on OS X is here: http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/ Happy Rcppin? Sincerely, JJB From: <rcpp-devel-bounces at lists.r-forge.r-project.org> on behalf of "aakremena at aol.com" <aakremena at aol.com> Date: Thursday, February 4, 2016 at 4:57 PM To: "rcpp-devel at lists.r-forge.r-project.org" <rcpp-devel at lists.r-forge.r-project.org> Subject: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so Hi everyone, My name is Anguel and I am new to this list. 1. I am trying to implement some simple example of a C++ compiled function from Hadley Wickham's website (http://adv-r.had.co.nz/Rcpp.html#rcpp). In fact the function I am trying to compile is the first one: library(Rcpp) cppFunction('int add(int x, int y, int z) { int sum = x + y + z; return sum;}') 2. Unfortunately I have immediately run into a problem, getting an error message: Error in dyn.load("/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so") : unable to load shared object '/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so': dlopen(/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib in /usr/local/lib/libquadmath.0.dylib 3. I am working on OS X Maverics (10.9.3) and I am using R3.2.0 platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 2.0 year 2015 month 04 day 16 svn rev 68180 language R version.string R version 3.2.0 (2015-04-16) nickname Full of Ingredients 4. I'm also using RcppArmadillo_0.6.500.4.0 and Rcpp_0.12.3 5. I can't seem to find any suggestions on the Internet concerning such a problem (maybe somebody will direct me in this regard). 6. I'll be extremely thankful to everybody who can direct me as to how to proceed from here. Of course, I'll be glad to provide any other information should you decide to answer my e-mail and request it. Thank you in advance. Anguel -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20160204/f1e2f472/attachment-0001.html>
Hi James and Dirk, James, I want to take the opportunity to thank you again for your competent advice. It worked. Dirk, does it seem like a reasonable suggestion to you to put the first of these links in your Rcpp FAQ file? This may go a long way to prevent some initial frustration with working with Rcpp for a OS X Maverick user. Thanks again. Anguel -----Original Message----- From: Balamuta, James Joseph <balamut2 at illinois.edu> To: aakremena <aakremena at aol.com>; rcpp-devel <rcpp-devel at lists.r-forge.r-project.org> Sent: Thu, Feb 4, 2016 5:58 pm Subject: Re: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so Greetings and Salutations, See: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/ Also, another example / more help setting up the dev environment on OS X is here: http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/ Happy Rcppin? Sincerely, JJB From: <rcpp-devel-bounces at lists.r-forge.r-project.org> on behalf of "aakremena at aol.com" <aakremena at aol.com> Date: Thursday, February 4, 2016 at 4:57 PM To: "rcpp-devel at lists.r-forge.r-project.org" <rcpp-devel at lists.r-forge.r-project.org> Subject: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so Hi everyone, My name is Anguel and I am new to this list. 1. I am trying to implement some simple example of a C++ compiled function from Hadley Wickham's website (http://adv-r.had.co.nz/Rcpp.html#rcpp). In fact the function I am trying to compile is the first one: library(Rcpp) cppFunction('int add(int x, int y, int z) { int sum = x + y + z; return sum;}') 2. Unfortunately I have immediately run into a problem, getting an error message: Error in dyn.load("/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so") : unable to load shared object '/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so': dlopen(/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so, 6): Symbol not found: ___addtf3 Referenced from: /usr/local/lib/libquadmath.0.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib in /usr/local/lib/libquadmath.0.dylib 3. I am working on OS X Maverics (10.9.3) and I am using R3.2.0 platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 2.0 year 2015 month 04 day 16 svn rev 68180 language R version.string R version 3.2.0 (2015-04-16) nickname Full of Ingredients 4. I'm also using RcppArmadillo_0.6.500.4.0 and Rcpp_0.12.3 5. I can't seem to find any suggestions on the Internet concerning such a problem (maybe somebody will direct me in this regard). 6. I'll be extremely thankful to everybody who can direct me as to how to proceed from here. Of course, I'll be glad to provide any other information should you decide to answer my e-mail and request it. Thank you in advance. Anguel -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20160205/8320f2ef/attachment.html>
Anguel, Thanks for taking the time to report back -- appreciated.
On 5 February 2016 at 11:19, aakremena at aol.com wrote:
| James, I want to take the opportunity to thank you again for your competent | advice. It worked. Seconded. | Dirk, does it seem like a reasonable suggestion to you to put the first of | these links in your Rcpp FAQ file? Yes -- right after James posted this I asked him off-list to take a look at what is currentlyn the Rcpp FAQ, which he very kindly agreed to do. The version is the package is stale-est, the one on GitHub received a recent updated -- but all this needs work. I'll also ping other OS X users like Kevin or Bob Rudis (who, if memory serves, recently wrote a 'R on OS X' checklist/howto). One idea could be to put something basic in the Rcpp FAQ and maybe link to the wiki within the Rcpp repo -- which we basically don't use at all right now -- to have a more dynamic reference too. Thoughts? | This may go a long way to prevent some initial frustration with working with | Rcpp for a OS X Maverick user. Absolutely. I am spoiled because things tend to 'just work' on Linux [1] so we all need to keep an eye on current and helpful OS X documentation. Ditto for Windows but Rtools is a bit standard(ized) already. Dirk [1] That is unless Ubuntu fscks up clang++ header use, but then again I mostly use g++. | | Thanks again. | | Anguel | | | | -----Original Message----- | From: Balamuta, James Joseph <balamut2 at illinois.edu> | To: aakremena <aakremena at aol.com>; rcpp-devel | <rcpp-devel at lists.r-forge.r-project.org> | Sent: Thu, Feb 4, 2016 5:58 pm | Subject: Re: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so | | Greetings and Salutations, | | See: | | http://thecoatlessprofessor.com/programming/ | rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/ | | Also, another example / more help setting up the dev environment on OS X is | here: | | http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/ | | Happy Rcppin? | | Sincerely, | | JJB | | | From: <rcpp-devel-bounces at lists.r-forge.r-project.org> on behalf of " | aakremena at aol.com" <aakremena at aol.com> | Date: Thursday, February 4, 2016 at 4:57 PM | To: "rcpp-devel at lists.r-forge.r-project.org" < | rcpp-devel at lists.r-forge.r-project.org> | Subject: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so | | Hi everyone, | | My name is Anguel and I am new to this list. | | 1. I am trying to implement some simple example of a C++ compiled function | from Hadley Wickham's website (http://adv-r.had.co.nz/Rcpp.html#rcpp). | In fact the function I am trying to compile is the first one: | | library(Rcpp) | cppFunction('int add(int x, int y, int z) { int sum = x + y + z; return sum;}') | | | | | | 2. Unfortunately I have immediately run into a problem, getting an error message: | | | | | Error in dyn.load("/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so") : | | | | | unable to load shared object '/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so': | | | | | dlopen(/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so, 6): Symbol not found: ___addtf3 | | | | | Referenced from: /usr/local/lib/libquadmath.0.dylib | | | | | Expected in: /usr/local/lib/libgcc_s.1.dylib | | | | | in /usr/local/lib/libquadmath.0.dylib | | | | | | 3. I am working on OS X Maverics (10.9.3) and I am using R3.2.0 | platform x86_64-apple-darwin13.4.0 | arch x86_64 | os darwin13.4.0 | system x86_64, darwin13.4.0 | status | major 3 | minor 2.0 | year 2015 | month 04 | day 16 | svn rev 68180 | language R | version.string R version 3.2.0 (2015-04-16) | nickname Full of Ingredients | | | | | | 4. I'm also using RcppArmadillo_0.6.500.4.0 and | | | | | | | Rcpp_0.12.3 | | | | | | | | 5. I can't seem to find any suggestions on the Internet concerning such a problem (maybe somebody will direct me in this regard). | | | | | | 6. I'll be extremely thankful to everybody who can direct me as to how to proceed from here. Of course, I'll be glad to provide any other information should you decide to answer my e-mail and request it. | | | | | | | | Thank you in advance. | | | | | | | Anguel | | | | | _______________________________________________ | Rcpp-devel mailing list | Rcpp-devel at lists.r-forge.r-project.org | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Hi Dirk and James,
Yes, I think this is a great idea
"One idea could be to put something basic in the Rcpp FAQ and maybe link to
the wiki within the Rcpp repo -- which we basically don't use at all right
now -- to have a more dynamic reference too. Thoughts?"
I think that "something basic" (like simply put the URL in the Rcpp FAQ) will be just fine. The idea is just to direct the OS X use that experienced "my" problem in the right direction.
Thanks again.
Anguel Grigorov
-----Original Message-----
From: Dirk Eddelbuettel <edd at debian.org>
To: aakremena <aakremena at aol.com>
Cc: balamut2 <balamut2 at illinois.edu>; rcpp-devel <rcpp-devel at lists.r-forge.r-project.org>
Sent: Fri, Feb 5, 2016 11:25 am
Subject: Re: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so
Anguel,
Thanks for taking the time to report back -- appreciated.
On 5 February 2016 at 11:19, aakremena at aol.com wrote:
| James, I want to take the opportunity to thank you again for your competent | advice. It worked. Seconded. | Dirk, does it seem like a reasonable suggestion to you to put the first of | these links in your Rcpp FAQ file? Yes -- right after James posted this I asked him off-list to take a look at what is currentlyn the Rcpp FAQ, which he very kindly agreed to do. The version is the package is stale-est, the one on GitHub received a recent updated -- but all this needs work. I'll also ping other OS X users like Kevin or Bob Rudis (who, if memory serves, recently wrote a 'R on OS X' checklist/howto). One idea could be to put something basic in the Rcpp FAQ and maybe link to the wiki within the Rcpp repo -- which we basically don't use at all right now -- to have a more dynamic reference too. Thoughts? | This may go a long way to prevent some initial frustration with working with | Rcpp for a OS X Maverick user. Absolutely. I am spoiled because things tend to 'just work' on Linux [1] so we all need to keep an eye on current and helpful OS X documentation. Ditto for Windows but Rtools is a bit standard(ized) already. Dirk [1] That is unless Ubuntu fscks up clang++ header use, but then again I mostly use g++. | | Thanks again. | | Anguel | | | | -----Original Message----- | From: Balamuta, James Joseph <balamut2 at illinois.edu> | To: aakremena <aakremena at aol.com>; rcpp-devel | <rcpp-devel at lists.r-forge.r-project.org> | Sent: Thu, Feb 4, 2016 5:58 pm | Subject: Re: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so | | Greetings and Salutations, | | See: | | http://thecoatlessprofessor.com/programming/ | rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/ | | Also, another example / more help setting up the dev environment on OS X is | here: | | http://thecoatlessprofessor.com/programming/r-compiler-tools-for-rcpp-on-os-x/ | | Happy Rcppin? | | Sincerely, | | JJB | | | From: <rcpp-devel-bounces at lists.r-forge.r-project.org> on behalf of " | aakremena at aol.com" <aakremena at aol.com> | Date: Thursday, February 4, 2016 at 4:57 PM | To: "rcpp-devel at lists.r-forge.r-project.org" < | rcpp-devel at lists.r-forge.r-project.org> | Subject: [Rcpp-devel] Rcpp problem related to sourceCpp_1.so | | Hi everyone, | | My name is Anguel and I am new to this list. | | 1. I am trying to implement some simple example of a C++ compiled function | from Hadley Wickham's website (http://adv-r.had.co.nz/Rcpp.html#rcpp). | In fact the function I am trying to compile is the first one: | | library(Rcpp) | cppFunction('int add(int x, int y, int z) { int sum = x + y + z; return sum;}') | | | | | | 2. Unfortunately I have immediately run into a problem, getting an error message: | | | | | Error in dyn.load("/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so") : | | | | | unable to load shared object '/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so': | | | | | dlopen(/var/folders/12/bqytpkx93w97r3s3_h9q9k_00000gn/T//RtmprqDXCj/sourcecpp_23c71c355072/sourceCpp_1.so, 6): Symbol not found: ___addtf3 | | | | | Referenced from: /usr/local/lib/libquadmath.0.dylib | | | | | Expected in: /usr/local/lib/libgcc_s.1.dylib | | | | | in /usr/local/lib/libquadmath.0.dylib | | | | | | 3. I am working on OS X Maverics (10.9.3) and I am using R3.2.0 | platform x86_64-apple-darwin13.4.0 | arch x86_64 | os darwin13.4.0 | system x86_64, darwin13.4.0 | status | major 3 | minor 2.0 | year 2015 | month 04 | day 16 | svn rev 68180 | language R | version.string R version 3.2.0 (2015-04-16) | nickname Full of Ingredients | | | | | | 4. I'm also using RcppArmadillo_0.6.500.4.0 and | | | | | | | Rcpp_0.12.3 | | | | | | | | 5. I can't seem to find any suggestions on the Internet concerning such a problem (maybe somebody will direct me in this regard). | | | | | | 6. I'll be extremely thankful to everybody who can direct me as to how to proceed from here. Of course, I'll be glad to provide any other information should you decide to answer my e-mail and request it. | | | | | | | | Thank you in advance. | | | | | | | Anguel | | | | | _______________________________________________ | Rcpp-devel mailing list | Rcpp-devel at lists.r-forge.r-project.org | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20160205/ec65d714/attachment-0001.html>