withr::set_makevars

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withr::set_makevars

Roy Mendelssohn - NOAA Federal
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@2dffbbe)            
 clisymbols     1.2.0       2017-09-02 Github (gaborcsardi/clisymbols@e49b4f5)  
 covr           3.0.0       2017-06-26 CRAN (R 3.4.1)                          
 crayon         1.3.2.9000  2017-08-25 Github (gaborcsardi/crayon@e4dba3b)      
 cyclocomp      1.1.0       2017-09-02 Github (MangoTheCat/cyclocomp@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@91490d1)        
 digest         0.6.12      2017-01-27 CRAN (R 3.4.1)                          
 goodpractice * 1.0.0       2017-09-02 Github (MangoTheCat/goodpractice@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@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@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@fd64bce)        
 rprojroot      1.2         2017-01-16 CRAN (R 3.4.0)                          
 rstudioapi     0.6.0.9000  2017-08-31 Github (rstudio/rstudioapi@e1e466b)      
 sessioninfo    1.0.1       2017-08-31 Github (r-lib/sessioninfo@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@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@ce3f15c)
 clisymbols     1.2.0      2017-06-10 Github (gaborcsardi/clisymbols@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@750190f)
 cyclocomp      1.1.0      2017-05-04 Github (MangoTheCat/cyclocomp@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@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@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@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@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: [hidden email] 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.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: withr::set_makevars

R help mailing list-2
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 <
[hidden email]> 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@2dffbbe)
>  clisymbols     1.2.0       2017-09-02 Github (gaborcsardi/clisymbols@
> e49b4f5)
>  covr           3.0.0       2017-06-26 CRAN (R 3.4.1)
>  crayon         1.3.2.9000  2017-08-25 Github (gaborcsardi/crayon@e4dba3b)
>  cyclocomp      1.1.0       2017-09-02 Github
> (MangoTheCat/cyclocomp@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@91490d1)
>  digest         0.6.12      2017-01-27 CRAN (R 3.4.1)
>  goodpractice * 1.0.0       2017-09-02 Github (MangoTheCat/goodpractice@
> 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@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@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@fd64bce)
>  rprojroot      1.2         2017-01-16 CRAN (R 3.4.0)
>  rstudioapi     0.6.0.9000  2017-08-31 Github (rstudio/rstudioapi@e1e466b)
>  sessioninfo    1.0.1       2017-08-31 Github (r-lib/sessioninfo@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@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@ce3f15c)
>  clisymbols     1.2.0      2017-06-10 Github (gaborcsardi/clisymbols@
> 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@750190f)
>  cyclocomp      1.1.0      2017-05-04 Github (MangoTheCat/cyclocomp@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@
> 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@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@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@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: [hidden email] 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.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: withr::set_makevars

Roy Mendelssohn - NOAA Federal
Perfect,  thank you very much for the tip.

-Roy

> On Sep 6, 2017, at 5:26 PM, William Dunlap <[hidden email]> 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 <http://tibco.com/>
> On Wed, Sep 6, 2017 at 3:41 PM, Roy Mendelssohn - NOAA Federal <[hidden email] <mailto:[hidden email]>> 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@2dffbbe)
>  clisymbols     1.2.0       2017-09-02 Github (gaborcsardi/clisymbols@e49b4f5)
>  covr           3.0.0       2017-06-26 CRAN (R 3.4.1)
>  crayon         1.3.2.9000  2017-08-25 Github (gaborcsardi/crayon@e4dba3b)
>  cyclocomp      1.1.0       2017-09-02 Github (MangoTheCat/cyclocomp@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@91490d1)
>  digest         0.6.12      2017-01-27 CRAN (R 3.4.1)
>  goodpractice * 1.0.0       2017-09-02 Github (MangoTheCat/goodpractice@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@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@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@fd64bce)
>  rprojroot      1.2         2017-01-16 CRAN (R 3.4.0)
>  rstudioapi     0.6.0.9000  2017-08-31 Github (rstudio/rstudioapi@e1e466b)
>  sessioninfo    1.0.1       2017-08-31 Github (r-lib/sessioninfo@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@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@ce3f15c)
>  clisymbols     1.2.0      2017-06-10 Github (gaborcsardi/clisymbols@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@750190f)
>  cyclocomp      1.1.0      2017-05-04 Github (MangoTheCat/cyclocomp@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@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@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@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@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: [hidden email] <mailto:[hidden email]> www: http://www.pfeg.noaa.gov/ <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.
>
> ______________________________________________
> [hidden email] <mailto:[hidden email]> mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help>
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html <http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>


        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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|

Re: withr::set_makevars

Roy Mendelssohn - NOAA Federal
In reply to this post by R help mailing list-2
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 <[hidden email]> 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 <[hidden email]> 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@2dffbbe)
>  clisymbols     1.2.0       2017-09-02 Github (gaborcsardi/clisymbols@e49b4f5)
>  covr           3.0.0       2017-06-26 CRAN (R 3.4.1)
>  crayon         1.3.2.9000  2017-08-25 Github (gaborcsardi/crayon@e4dba3b)
>  cyclocomp      1.1.0       2017-09-02 Github (MangoTheCat/cyclocomp@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@91490d1)
>  digest         0.6.12      2017-01-27 CRAN (R 3.4.1)
>  goodpractice * 1.0.0       2017-09-02 Github (MangoTheCat/goodpractice@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@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@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@fd64bce)
>  rprojroot      1.2         2017-01-16 CRAN (R 3.4.0)
>  rstudioapi     0.6.0.9000  2017-08-31 Github (rstudio/rstudioapi@e1e466b)
>  sessioninfo    1.0.1       2017-08-31 Github (r-lib/sessioninfo@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@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@ce3f15c)
>  clisymbols     1.2.0      2017-06-10 Github (gaborcsardi/clisymbols@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@750190f)
>  cyclocomp      1.1.0      2017-05-04 Github (MangoTheCat/cyclocomp@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@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@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@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@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: [hidden email] 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.
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> 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: [hidden email] 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.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.