[R] withr::set_makevars
Roy Mendelssohn - NOAA Federal
roy.mendelssohn at noaa.gov
Sat Sep 9 22:01:00 CEST 2017
As a follow-up to this, thanks to Bill Dunlap I was able to resolve what was causing this problem (I still had problems with covr::package_coverage() - but of a different sort and not directly related to this report, I had an existing .R/Makevars file, created in Nov. 2014 related to the installation of the rstan package. Commenting out some of the rstan specific lines removed this set of error messages.
-Roy
> On Sep 6, 2017, at 5:26 PM, William Dunlap <wdunlap at tibco.com> wrote:
>
> withr:::set_makevars() can give that error if the makefile named by the 'old_path' argument (default "~/.R/Makevars) contains more than one definition of a variable of the form 'name=value'. You can see what file it is reading and its contents by using the trace() function:
>
> trace(withr:::set_makevars, quote({ cat(old_path, "\n"); writeLines(paste0(" ", tryCatch(readLines(old_path), error=function(e)conditionMessage(e))))}))
>
> Then run your test and see what file set_makevars is complaining about and what in the file might cause trouble for set_makevars.
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Wed, Sep 6, 2017 at 3:41 PM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
> Hi All;
>
> This problem has come about from trying to learn some of the review practices recommend by rOpensci. One of them is to use the package goodpractice. After installing goodpractice, it kept failing on my own packages which are under development, and I was concerned something was funny in my own , so I have a fork of the package rerddap, and I tested goodpractice on that. I get the error:
>
> > Error in set_makevars(new, path, makevars_file, assignment = assignment) :
> > Multiple results for CXXFLAGS found, something is wrong.FALSE
> >
>
>
> So after some playing around that is from the very first test, which uses the covr:package_coverage(), and sure enough running that produces the same error. Looking at the code, that error is being thrown by the function withr::set_makevars(). We are now too many layers deep into packages for me to follow what is going on, but the kicker is Scott Chamberlain can run it without any errors on the same package. Session_info for both of us follows. If any one has any suggestions both as to what is causing this and a possible solution, would appreciate it.
>
> Roy's sessionInfo is after running the commands:
>
> Sys.setenv(NOT_CRAN = "true")
> x = goodpractice::gp(path = ".", checks = all_checks()[2:230])
>
> Scott's is after running:
>
> Sys.setenv(NOT_CRAN = "true")
> x = goodpractice::gp()
>
>
>
>
> Roy's_session_info()
> ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
> setting value
> version R version 3.4.1 (2017-06-30)
> os macOS Sierra 10.12.6
> system x86_64, darwin15.6.0
> ui RStudio
> language (EN)
> collate en_US.UTF-8
> tz America/Los_Angeles
> date 2017-09-06
>
> ─ Packages package * version date source
> assertthat 0.2.0 2017-04-11 CRAN (R 3.4.1)
> backports 1.1.0 2017-05-22 CRAN (R 3.4.0)
> callr 1.0.0.9000 2017-09-02 Github (r-lib/callr at 2dffbbe)
> clisymbols 1.2.0 2017-09-02 Github (gaborcsardi/clisymbols at e49b4f5)
> covr 3.0.0 2017-06-26 CRAN (R 3.4.1)
> crayon 1.3.2.9000 2017-08-25 Github (gaborcsardi/crayon at e4dba3b)
> cyclocomp 1.1.0 2017-09-02 Github (MangoTheCat/cyclocomp at 6156a12)
> debugme 1.0.2 2017-03-01 CRAN (R 3.4.0)
> desc 1.1.1 2017-08-03 CRAN (R 3.4.1)
> devtools 1.13.3.9000 2017-08-31 Github (hadley/devtools at 91490d1)
> digest 0.6.12 2017-01-27 CRAN (R 3.4.1)
> goodpractice * 1.0.0 2017-09-02 Github (MangoTheCat/goodpractice at 9969799)
> httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
> igraph 1.1.2 2017-07-21 CRAN (R 3.4.1)
> jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
> knitr 1.17 2017-08-10 CRAN (R 3.4.1)
> lazyeval 0.2.0 2016-06-12 CRAN (R 3.4.0)
> lintr 1.0.1 2017-08-10 CRAN (R 3.4.1)
> magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
> memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
> pkgbuild 0.0.0.9000 2017-08-31 Github (r-lib/pkgbuild at 6574561)
> pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
> pkgload 0.0.0.9000 2017-08-31 Github (r-pkgs/pkgload at 80a6493)
> praise 1.0.0 2015-08-11 CRAN (R 3.4.0)
> processx 2.0.0.1 2017-07-30 CRAN (R 3.4.1)
> R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
> rcmdcheck 1.2.1 2016-09-28 CRAN (R 3.4.0)
> Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1)
> remotes 1.1.0 2017-07-09 CRAN (R 3.4.1)
> rex 1.1.1 2016-12-05 CRAN (R 3.4.0)
> rlang 0.1.2.9000 2017-09-05 Github (tidyverse/rlang at fd64bce)
> rprojroot 1.2 2017-01-16 CRAN (R 3.4.0)
> rstudioapi 0.6.0.9000 2017-08-31 Github (rstudio/rstudioapi at e1e466b)
> sessioninfo 1.0.1 2017-08-31 Github (r-lib/sessioninfo at e813de4)
> stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
> stringr 1.2.0 2017-02-18 CRAN (R 3.4.0)
> usethis 0.0.0.9000 2017-08-31 Github (r-lib/usethis at 12e6f95)
> whoami 1.1.1 2015-07-13 CRAN (R 3.4.0)
> withr 2.0.0 2017-07-28 CRAN (R 3.4.1)
> xml2 1.1.1 2017-01-24 CRAN (R 3.4.0)
> xmlparsedata 1.0.1 2016-06-18 CRAN (R 3.4.0)
> yaml 2.1.14 2016-11-12 CRAN (R 3.4.0)
>
>
> Scott's _ sessionInfo()
> Session info ------------------------------------------------------------------
> setting value
> version R version 3.4.1 Patched (2017-07-04 r72893)
> system x86_64, darwin15.6.0
> ui X11
> language (EN)
> collate en_US.UTF-8
> tz America/Los_Angeles
> date 2017-09-06
>
> Packages ----------------------------------------------------------------------
> package * version date source
> assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
> backports 1.1.0 2017-05-22 CRAN (R 3.4.0)
> base * 3.4.1 2017-07-06 local
> callr 1.0.0.9000 2017-07-31 Github (r-lib/callr at ce3f15c)
> clisymbols 1.2.0 2017-06-10 Github (gaborcsardi/clisymbols at 83b13a0)
> compiler 3.4.1 2017-07-06 local
> covr 3.0.0 2017-06-26 CRAN (R 3.4.0)
> crayon 1.3.2.9000 2017-07-31 Github (gaborcsardi/crayon at 750190f)
> cyclocomp 1.1.0 2017-05-04 Github (MangoTheCat/cyclocomp at 6156a12)
> datasets * 3.4.1 2017-07-06 local
> debugme 1.0.2 2017-03-01 cran (@1.0.2)
> desc 1.1.1 2017-08-03 CRAN (R 3.4.1)
> devtools * 1.13.3 2017-08-02 CRAN (R 3.4.1)
> digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
> goodpractice 1.0.0 2017-06-10 Github (MangoTheCat/goodpractice at 9969799)
> graphics * 3.4.1 2017-07-06 local
> grDevices * 3.4.1 2017-07-06 local
> httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
> jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
> lazyeval 0.2.0 2016-06-12 CRAN (R 3.4.0)
> lintr 1.0.1 2017-08-10 CRAN (R 3.4.1)
> magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
> memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
> methods * 3.4.1 2017-07-06 local
> praise 1.0.0 2015-08-11 CRAN (R 3.4.0)
> prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.0)
> processx 2.0.1.9000 2017-07-31 Github (r-lib/processx at c02b0f3)
> R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
> rcmdcheck 1.2.1.9000 2017-06-10 Github (r-pkgs/rcmdcheck at a18119c)
> Rcpp 0.12.12 2017-07-15 cran (@0.12.12)
> remotes 1.1.0 2017-07-09 CRAN (R 3.4.1)
> rex 1.1.1 2016-03-11 CRAN (R 3.4.0)
> rprojroot 1.2 2017-01-16 CRAN (R 3.4.0)
> rstudioapi 0.6 2016-06-27 CRAN (R 3.4.0)
> stats * 3.4.1 2017-07-06 local
> tools 3.4.1 2017-07-06 local
> utils * 3.4.1 2017-07-06 local
> whoami 1.1.1 2015-07-13 CRAN (R 3.4.0)
> withr 2.0.0 2017-09-05 Github (jimhester/withr at eff4818)
> xml2 1.1.1 2017-01-24 CRAN (R 3.4.0)
> xmlparsedata 1.0.1 2016-06-18 cran (@1.0.1)
>
>
> **********************
> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>
**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
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