[R] withr::set_makevars
Roy Mendelssohn - NOAA Federal
roy.mendelssohn at noaa.gov
Thu Sep 7 00:41:56 CEST 2017
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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