[Rd] Compiling on AIX 6.1
I'm trying to compile R on AIX 6.1. gcc -v Using built-in specs. Target: powerpc-ibm-aix6.1.0.0 Configured with: ../gcc-4.4.5/configure --with-as=/usr/bin/as --with-ld=/usr/bin/ld --enable-languages=c,c++,fortran --prefix=/opt/freeware --enable-threads --enable-version-specific-runtime-libs --disable-nls --enable-decimal-float=dpd --host=powerpc-ibm-aix6.1.0.0 Thread model: aix gcc version 4.4.5 (GCC) gfortran -v Using built-in specs. Target: powerpc-ibm-aix6.1.0.0 Configured with: ../gcc-4.4.5/configure --with-as=/usr/bin/as --with-ld=/usr/bin/ld --enable-languages=c,c++,fortran --prefix=/opt/freeware --enable-threads --enable-version-specific-runtime-libs --disable-nls --enable-decimal-float=dpd --host=powerpc-ibm-aix6.1.0.0 Thread model: aix gcc version 4.4.5 (GCC) No matter what I try, I keep getting the following errors. ld: 0711-224 WARNING: Duplicate symbol: R_ReadItemDepth ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. ld: 0711-317 ERROR: Undefined symbol: .__nearbyintl128 ld: 0711-317 ERROR: Undefined symbol: .__log1pl128 collect2: ld returned 8 exit status make: 1254-004 The error code from the last command is 1. Any ideas on how to correct this? Thanks Phil Phillip Schermerhorn Programmer/Analyst Communication Technology Management -- City of Austin Office: (512) 974-1433 The latest survey shows that three out of four people make up 75% of the population. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD build failure
I have a local library 'dart' that imports "httr". It has routines that access central patient data such as birth date, so it is heavily used locally but of no interest to anyone else. The httr library (and 300 others) are in a shared directory, referenced by everyone in the biostatistics group via adding this location to the .libPaths in their default .Rprofile. (Actually, their .Rprofile starts by running material from a central one, the libPaths is there). When I run R (3.2.0) all is fine, but R CMD build fails with the text below * creating vignettes ... ERROR Error: processing vignette 'dart.Rnw' failed with diagnostics: chunk 2 (label = auth1) Error : package ‘httr’ required by ‘dart’ could not be found Execution halted If I add the requiste directory to my R_LIBS_USER environment variable then all is fine. However, that's a nuisance since the location changes over time (e.g. R releases). The system admins have a whole process that keeps .bashrc, .Rprofle and etc dot references up to date. Plugging into this is why we use .Rprofile. They are quite willing to make select changes in the central file, but with >1000 users any suggested changes in the overall process do not get a warm welcome. Any ideas? There is no mention in the Writing R Extentions manual that it ignores the Rprofile file. If "suck it up and use R_LIBS_USER" is the answer, well, there are only a few who build packages. PS, I can't use RHOME:/etc/Rprofile.site since the biostat group is not the only set of R users. Some other groups, for instance, cannot even see our central area. Terry T. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build failure
What field is httr in the DESCRIPTION? Hadley On Thu, Jul 9, 2015 at 10:26 AM, Therneau, Terry M., Ph.D. wrote: > I have a local library 'dart' that imports "httr". It has routines that > access central patient data such as birth date, so it is heavily used > locally but of no interest to anyone else. > > The httr library (and 300 others) are in a shared directory, referenced by > everyone in the biostatistics group via adding this location to the > .libPaths in their default .Rprofile. (Actually, their .Rprofile starts by > running material from a central one, the libPaths is there). > > When I run R (3.2.0) all is fine, but R CMD build fails with the text below > > * creating vignettes ... ERROR > Error: processing vignette 'dart.Rnw' failed with diagnostics: > chunk 2 (label = auth1) > Error : package ‘httr’ required by ‘dart’ could not be found > Execution halted > > > If I add the requiste directory to my R_LIBS_USER environment variable then > all is fine. However, that's a nuisance since the location changes over > time (e.g. R releases). The system admins have a whole process that keeps > .bashrc, .Rprofle and etc dot references up to date. Plugging into this is > why we use .Rprofile. They are quite willing to make select changes in the > central file, but with >1000 users any suggested changes in the overall > process do not get a warm welcome. > > Any ideas? There is no mention in the Writing R Extentions manual that it > ignores the Rprofile file. If "suck it up and use R_LIBS_USER" is the > answer, well, there are only a few who build packages. > > PS, I can't use RHOME:/etc/Rprofile.site since the biostat group is not the > only set of R users. Some other groups, for instance, cannot even see our > central area. > > Terry T. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build failure
"Depends: httr (>= 0.6), XML" in the DESCRIPTION file "import(httr, XML)" in NAMESPACE Per your question I just tried changing "Depends" to "Imports", it didn't make a change. Terry T. On 07/09/2015 12:33 PM, Hadley Wickham wrote: What field is httr in the DESCRIPTION? Hadley On Thu, Jul 9, 2015 at 10:26 AM, Therneau, Terry M., Ph.D. wrote: I have a local library 'dart' that imports "httr". It has routines that access central patient data such as birth date, so it is heavily used locally but of no interest to anyone else. The httr library (and 300 others) are in a shared directory, referenced by everyone in the biostatistics group via adding this location to the .libPaths in their default .Rprofile. (Actually, their .Rprofile starts by running material from a central one, the libPaths is there). When I run R (3.2.0) all is fine, but R CMD build fails with the text below * creating vignettes ... ERROR Error: processing vignette 'dart.Rnw' failed with diagnostics: chunk 2 (label = auth1) Error : package ‘httr’ required by ‘dart’ could not be found Execution halted If I add the requiste directory to my R_LIBS_USER environment variable then all is fine. However, that's a nuisance since the location changes over time (e.g. R releases). The system admins have a whole process that keeps .bashrc, .Rprofle and etc dot references up to date. Plugging into this is why we use .Rprofile. They are quite willing to make select changes in the central file, but with >1000 users any suggested changes in the overall process do not get a warm welcome. Any ideas? There is no mention in the Writing R Extentions manual that it ignores the Rprofile file. If "suck it up and use R_LIBS_USER" is the answer, well, there are only a few who build packages. PS, I can't use RHOME:/etc/Rprofile.site since the biostat group is not the only set of R users. Some other groups, for instance, cannot even see our central area. Terry T. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build failure
On Thu, 9 Jul 2015, Therneau, Terry M., Ph.D. wrote: I have a local library 'dart' that imports "httr". [snip `R CMD build' can't find dart] Any ideas? There is no mention in the Writing R Extentions manual that it ignores the Rprofile file. Terry, From WRE: 1.3 Checking and building packages ... Note: R CMD check and R CMD build run R processes with --vanilla in which none of the user’s startup files are read. If you need R_LIBS set (to find packages in a non-standard library) you can set it in the environment: also you can use the check and build environment files (as specified by the environment variables R_CHECK_ENVIRON and R_BUILD_ENVIRON; if unset, files33 ~/.R/check.Renviron and ~/.R/build.Renviron are used) to set environment variables when using these utilities. And from ?Startup The command-line option --vanilla implies --no-site-file, --no-init-file, --no-environ and (except for R CMD) --no-restore HTH, Chuck __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build failure
On Thu, Jul 9, 2015 at 12:26 PM, Therneau, Terry M., Ph.D. wrote: > I have a local library 'dart' that imports "httr". It has routines that > access central patient data such as birth date, so it is heavily used > locally but of no interest to anyone else. > > The httr library (and 300 others) are in a shared directory, referenced by > everyone in the biostatistics group via adding this location to the > .libPaths in their default .Rprofile. (Actually, their .Rprofile starts by > running material from a central one, the libPaths is there). > > When I run R (3.2.0) all is fine, but R CMD build fails with the text below > > * creating vignettes ... ERROR > Error: processing vignette 'dart.Rnw' failed with diagnostics: > chunk 2 (label = auth1) > Error : package ‘httr’ required by ‘dart’ could not be found > Execution halted > > > If I add the requiste directory to my R_LIBS_USER environment variable then > all is fine. However, that's a nuisance since the location changes over > time (e.g. R releases). The system admins have a whole process that keeps > .bashrc, .Rprofle and etc dot references up to date. Plugging into this is > why we use .Rprofile. They are quite willing to make select changes in the > central file, but with >1000 users any suggested changes in the overall > process do not get a warm welcome. > > Any ideas? There is no mention in the Writing R Extentions manual that it > ignores the Rprofile file. If "suck it up and use R_LIBS_USER" is the > answer, well, there are only a few who build packages. > It is mentioned in ?Startup: "'R CMD check' and 'R CMD build' do not always read the standard startup files, but they do always read specific 'Renviron' files. The location of these can be controlled by the environment variables 'R_CHECK_ENVIRON' and 'R_BUILD_ENVIRON'. If these are set their value is used as the path for the 'Renviron' file; otherwise, files '~/.R/check.Renviron' or '~/.R/build.Renviron' or sub-architecture-specific versions are employed." Maybe one of those options could work for you? > PS, I can't use RHOME:/etc/Rprofile.site since the biostat group is not the > only set of R users. Some other groups, for instance, cannot even see our > central area. > > Terry T. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
