search for: biostat2

...cess. 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 Platform: x86_64-pc-linux-gnu (64-bit) > 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? 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 libra...

...he following sequence works: tmt% R CMD build --no-build-vignettes hmm tmt% R CMD INSTALL hmm*gz tmt% R > library(hmm) > run some commands from the hmm library But "R CMD check hmm.gz" fails with ERROR: dependency ?expm? is not available for package ?hmm? * removing ?/people/biostat2/therneau/consult/alzheimer/hmm.Rcheck/hmm? The R CMD build command fails similarly if I let it try to build the vignettes. What's up? Terry T > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final)

...s. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > dyn.load('survival.so') Error in dyn.load("survival.so") : unable to load shared object '/people/biostat2/therneau/research/surv/Rtest/survival.so': libR.so: cannot open shared object file: No such file or directory > q() -------------------------- Is the issue that the .so file must have been created with the R2.13 script? That's not what the error message says, however. It almost lo...

...ron > > R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" > Copyright (C) 2016 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > > > > 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 Plu...

...ses some cross-calls to it's C routines, which have been exported using the R_RegisterCCallable function. All works as expected: modules load, tests succeed. Running R CMD check fails however, tmt703% R CMD check coxme * checking for working pdflatex ... OK * using log directory '/people/biostat2/therneau/research/surv/Rforge/pkg/coxme.Rcheck' * using R version 2.9.0 (2009-04-17) * using session charset: UTF-8 * checking for file 'coxme/DESCRIPTION' ... OK * this is package 'coxme' version '1.0' * checking package name space information ... OK * checking package...

...3.3.1 (2016-06-21) -- "Bug in Your Hair" >> Copyright (C) 2016 The R Foundation for Statistical Computing >> Platform: x86_64-pc-linux-gnu (64-bit) >> >>> >>> 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....

...d --no-build-vignettes hmm > tmt% R CMD INSTALL hmm*gz > tmt% R > ?> library(hmm) > ?>??run some commands from the hmm library > > But "R CMD check hmm.gz" fails with > ???ERROR: dependency ?expm? is not available for package ?hmm? > * removing > ?/people/biostat2/therneau/consult/alzheimer/hmm.Rcheck/hmm? > > The R CMD build command fails similarly if I let it try to build the > vignettes. > > What's up? If you are setting the environment variable R_LIBS_USER in R_HOME/site/Renviron.site or in .Renviron then this file will not be read...