search for: r_check_environ

...ails upon not finding the dependencies which I have installed in a non-standard location. Per the manual, I created ~/.R/check.Renviron : $ cat ~/.R/check.Renviron R_LIBS=/usr/lib64/R/library:/usr/lib64/R/var R_LIBS_SITE=/usr/lib64/R/library:/usr/lib64/R/var No luck. I tried explicitly pointing R_CHECK_ENVIRON to ~/.R/check.Renviron: $ echo $R_CHECK_ENVIRON /root/.R/check.Renviron Still no luck. Finally, I just set R_LIBS globally (which, was empty) before running the check and the dependencies are then found. Just wanted to be sure I'm not missing something before creating a bug report. This is...

...evant directory. R CMD build *does* read R_LIBS from ~/.R/build.Renviron for the same versions of R on the same Fedora 16 laptop. So I am in the strange situation of being able to build but not check a source package having followed the instructions in Writing R Extensions. I have tried exporting R_CHECK_ENVIRON via export R_CHECK_ENVIRON=/home/gavin/.R/check.Renviron and that doesn't work either. ~/.R/check.Renviron contains: R_LIBS=/home/gavin/R/libs/ #R_LIBS=/home/gavin/R/devlibs/ Anyone suggest how/where I am going wrong? More complete system info follows below. TIA Gavin > sessionI...

...e that there are no other versions of vegan inadvertently installed to the build directory for R Under Development. Following advice in Writing R Extensions I have also created ~/build.Renviron and ~/check.Renviron and as these are non-standard I also followed the advice to set R_BUILD_ENVIRON and R_CHECK_ENVIRON again temporarily via export: $ cat $R_CHECK_ENVIRON R_LIBS=/home/gavin/R/devlibs $ cat $R_BUILD_ENVIRON R_LIBS=/home/gavin/R/devlibs Yet still I get errors building analogue: $ Rdevel CMD build ../analogue/pkg/ * checking for file ?../analogue/pkg/DESCRIPTION? ... OK * preparing ?analogue?: *...

Martin, I am aware of --vanilla; I use it myself for some testing. In this case R_LIBS_USER was set externally (part of my login) and does not involve any of the R scripts. That means it is inherited by any subprocess. For example: tmt1495% R --vanilla --no-environ R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing

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.

...; > > > system("printenv | grep R_LIBS") > R_LIBS_SITE= > R_LIBS_USER=/people/biostat2/therneau/Rlib > > So, per the manual R CMD check inherits the path.??The question is > why does it ignore it? Hmmm. Perhaps it is being overwritten. ?Does this work? $ export R_CHECK_ENVIRON= $ R CMD check hmm.gz Martyn > Terry T. > > > On 02/09/2017 02:54 AM, Martyn Plummer wrote: > > > > On Wed, 2017-02-08 at 15:51 -0600, Therneau, Terry M., Ph.D. wrote: > > > > > > I have a local library which depends on the expm library.??The expm lib...

...nv | grep R_LIBS") >> R_LIBS_SITE= >> R_LIBS_USER=/people/biostat2/therneau/Rlib >> >> So, per the manual R CMD check inherits the path. The question is >> why does it ignore it? > > Hmmm. Perhaps it is being overwritten. Does this work? > > $ export R_CHECK_ENVIRON= > $ R CMD check hmm.gz > > Martyn > >> Terry T. >> >> >> On 02/09/2017 02:54 AM, Martyn Plummer wrote: >>> >>> On Wed, 2017-02-08 at 15:51 -0600, Therneau, Terry M., Ph.D. wrote: >>>> >>>> I have a local library which de...

I knew I could work around. But this shouldn't happen. And yes. Same problem with your example. blurfle$ R --vanilla R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain

...compiled code, and has been able to find the .o file in which the calls occur. Such calls can terminate the R process which loads the package. o The location of the build and check environment files can now be specified by the environment variables R_BUILD_ENVIRON and R_CHECK_ENVIRON, respectively. o R CMD Sweave gains a --compact option to control possibly reducing the size of the PDF file it creates when --pdf is given. o R CMD build now omits Eclipse's .metadata directories, and R CMD check warns if it finds them. o R CMD check now does some ch...

...compiled code, and has been able to find the .o file in which the calls occur. Such calls can terminate the R process which loads the package. o The location of the build and check environment files can now be specified by the environment variables R_BUILD_ENVIRON and R_CHECK_ENVIRON, respectively. o R CMD Sweave gains a --compact option to control possibly reducing the size of the PDF file it creates when --pdf is given. o R CMD build now omits Eclipse's .metadata directories, and R CMD check warns if it finds them. o R CMD check now does some ch...