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.
What field is httr in the DESCRIPTION? Hadley On Thu, Jul 9, 2015 at 10:26 AM, Therneau, Terry M., Ph.D. <therneau at mayo.edu> 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 at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- http://had.co.nz/
"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. > <therneau at mayo.edu> 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 at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > >
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
On Thu, Jul 9, 2015 at 12:26 PM, Therneau, Terry M., Ph.D. <therneau at mayo.edu> 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 at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com