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Closing out improvements from the Try-6 Branch and merging to master #29

Closed dwbapst closed 5 years ago

dwbapst commented 5 years ago

Should push things to master, realllly...

Fixes #23 Fixes #28 Fixes #30

codecov[bot] commented 5 years ago

Codecov Report

Merging #29 into master will decrease coverage by 1.1%. The diff coverage is 60.63%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #29      +/-   ##
==========================================
- Coverage   71.29%   70.18%   -1.11%     
==========================================
  Files          37       40       +3     
  Lines        2212     2472     +260     
==========================================
+ Hits         1577     1735     +158     
- Misses        635      737     +102
Impacted Files Coverage Δ
R/internal.abcparticle.R 100% <ø> (+14.1%) :arrow_up:
R/PairwiseESS.R 100% <ø> (ø) :arrow_up:
R/multiOptimaIntrinsic.R 0% <0%> (ø) :arrow_up:
R/internal.postRunSimulateFromMeans.R 0% <0%> (ø)
R/internal.abctaxon.R 100% <100%> (ø) :arrow_up:
R/internal.registerMulticoreEnv.R 60.6% <100%> (ø) :arrow_up:
R/doRun_rej.R 88.04% <100%> (ø) :arrow_up:
R/internal.rnormFastZig.R 100% <100%> (ø)
R/doSimulation.R 81.55% <100%> (+0.94%) :arrow_up:
R/internal.getFreeVector.R 82.35% <100%> (+3.28%) :arrow_up:
... and 11 more

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 50e4ffc...efc5821. Read the comment docs.

codecov[bot] commented 5 years ago

Codecov Report

Merging #29 into master will decrease coverage by 1.1%. The diff coverage is 60.63%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #29      +/-   ##
==========================================
- Coverage   71.29%   70.18%   -1.11%     
==========================================
  Files          37       40       +3     
  Lines        2212     2472     +260     
==========================================
+ Hits         1577     1735     +158     
- Misses        635      737     +102
Impacted Files Coverage Δ
R/internal.abcparticle.R 100% <ø> (+14.1%) :arrow_up:
R/PairwiseESS.R 100% <ø> (ø) :arrow_up:
R/multiOptimaIntrinsic.R 0% <0%> (ø) :arrow_up:
R/internal.postRunSimulateFromMeans.R 0% <0%> (ø)
R/internal.abctaxon.R 100% <100%> (ø) :arrow_up:
R/internal.registerMulticoreEnv.R 60.6% <100%> (ø) :arrow_up:
R/doRun_rej.R 88.04% <100%> (ø) :arrow_up:
R/internal.rnormFastZig.R 100% <100%> (ø)
R/doSimulation.R 81.55% <100%> (+0.94%) :arrow_up:
R/internal.getFreeVector.R 82.35% <100%> (+3.28%) :arrow_up:
... and 11 more

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 50e4ffc...efc5821. Read the comment docs.

codecov[bot] commented 5 years ago

Codecov Report

Merging #29 into master will decrease coverage by 1.1%. The diff coverage is 60.63%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #29      +/-   ##
==========================================
- Coverage   71.29%   70.18%   -1.11%     
==========================================
  Files          37       40       +3     
  Lines        2212     2472     +260     
==========================================
+ Hits         1577     1735     +158     
- Misses        635      737     +102
Impacted Files Coverage Δ
R/internal.abcparticle.R 100% <ø> (+14.1%) :arrow_up:
R/PairwiseESS.R 100% <ø> (ø) :arrow_up:
R/multiOptimaIntrinsic.R 0% <0%> (ø) :arrow_up:
R/internal.postRunSimulateFromMeans.R 0% <0%> (ø)
R/internal.abctaxon.R 100% <100%> (ø) :arrow_up:
R/internal.registerMulticoreEnv.R 60.6% <100%> (ø) :arrow_up:
R/doRun_rej.R 88.04% <100%> (ø) :arrow_up:
R/internal.rnormFastZig.R 100% <100%> (ø)
R/doSimulation.R 81.55% <100%> (+0.94%) :arrow_up:
R/internal.getFreeVector.R 82.35% <100%> (+3.28%) :arrow_up:
... and 11 more

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 50e4ffc...efc5821. Read the comment docs.

dwbapst commented 5 years ago

Passes with donttest examples run

dwbapst commented 5 years ago 

> 
> devtools::check("d://dave//workspace//treevo", 
+ manual=TRUE, remote=TRUE, run_dont_test = TRUE)
Updating TreEvo documentation
Writing NAMESPACE
Loading TreEvo
Writing NAMESPACE
-- Building ---------------------------------------------------------- TreEvo --
Setting env vars:
* CFLAGS    : -Wall -pedantic
* CXXFLAGS  : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
--------------------------------------------------------------------------------
   checking for file 'd:\dave\workspace\treevo/DESCRIPTION' ...
   checking for file 'd:\dave\workspace\treevo/DESCRIPTION' ... 
√  checking for file 'd:\dave\workspace\treevo/DESCRIPTION'
-  preparing 'TreEvo': (4.4s)
   checking DESCRIPTION meta-information ...
   checking DESCRIPTION meta-information ... 
√  checking DESCRIPTION meta-information
-  installing the package to build vignettes
   creating vignettes ...
   creating vignettes ... 
√  creating vignettes (10s)
-  checking for LF line-endings in source and make files and shell scripts (3.4s)
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'TreEvo_0.20.3.tar.gz'
-- Checking ---------------------------------------------------------- TreEvo --
Setting env vars:
* _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
* _R_CHECK_CRAN_INCOMING_REMOTE_    : TRUE
* _R_CHECK_CRAN_INCOMING_           : TRUE
* _R_CHECK_FORCE_SUGGESTS_          : FALSE
-- R CMD check ------------------------------------------------------------------  
-  using log directory 'C:/Users/dwbapst/AppData/Local/Temp/RtmpEBgWZV/TreEvo.Rcheck'
-  using R version 3.5.2 (2018-12-20)
--  using platform: x86_64-w64-mingw32 (64-bit)
-  using session charset: ISO8859-1
  --  using options '--run-donttest --as-cran'
   checking for file 'TreEvo/DESCRIPTION' ...-
   checking for file 'TreEvo/DESCRIPTION' ... 
√  checking for file 'TreEvo/DESCRIPTION'
     checking extension type ... Package
     this is package 'TreEvo' version '0.20.3'
   package encoding: UTF-8
   checking CRAN incoming feasibility ...
   checking CRAN incoming feasibility ... 
N  checking CRAN incoming feasibility (1m 26.7s)
   Maintainer: 'David Bapst <dwbapst@gmail.com>'
   New submission
   checking package namespace information ...-√  checking package namespace information
   checking package dependencies ...
   checking package dependencies ... -N  checking package dependencies (2.8s)
   Packages suggested but not available for checking: 'doMC' 'gpclib'
   checking if this is a source package ...
   checking if this is a source package ... -√  checking if this is a source package
   checking if there is a namespace ...
√  checking if there is a namespace
   checking for executable files ...
   checking for executable files ... 
√  checking for executable files (535ms)
   checking for hidden files and directories ...
   checking for hidden files and directories ... 
√  checking for hidden files and directories
   checking for portable file names ...-
   checking for portable file names ... 
√  checking for portable file names-  
   checking serialization versions ...-
   checking serialization versions ... 
√  checking serialization versions
   checking whether package 'TreEvo' can be installed ...
   checking whether package 'TreEvo' can be installed ... 
√  checking whether package 'TreEvo' can be installed (8.3s)
   checking installed package size ...
   checking installed package size ... -√  checking installed package size
√  checking package directory (343ms)
√  checking 'build' directory
   checking DESCRIPTION meta-information ...
   checking DESCRIPTION meta-information ... 
√  checking DESCRIPTION meta-information (365ms)
   checking top-level files ...
   checking top-level files ... -√  checking top-level files (1.2s)
   checking for left-over files ...
   checking for left-over files ... -√  checking for left-over files
   checking index information ...
   checking index information ... 
√  checking index information
   checking package subdirectories ...
   checking package subdirectories ... 
√  checking package subdirectories (489ms)
   checking R files for non-ASCII characters ...
   checking R files for non-ASCII characters ... 
√  checking R files for non-ASCII characters
   checking R files for syntax errors ...
   checking R files for syntax errors ... 
√  checking R files for syntax errors
   checking whether the package can be loaded ...
   checking whether the package can be loaded ... 
√  checking whether the package can be loaded (1.8s)
   checking whether the package can be loaded with stated dependencies ...
   checking whether the package can be loaded with stated dependencies ... 
√  checking whether the package can be loaded with stated dependencies (1.6s)
   checking whether the package can be unloaded cleanly ...
   checking whether the package can be unloaded cleanly ... -
√  checking whether the package can be unloaded cleanly (1.6s)
   checking whether the namespace can be loaded with stated dependencies ...
   checking whether the namespace can be loaded with stated dependencies ... 
√  checking whether the namespace can be loaded with stated dependencies (1.9s)
   checking whether the namespace can be unloaded cleanly ...
   checking whether the namespace can be unloaded cleanly ... 
√  checking whether the namespace can be unloaded cleanly (1.7s)
-   checking loading without being on the library search path ...
   checking loading without being on the library search path ... 
√  checking loading without being on the library search path (1.9s)
   checking use of S3 registration ...
   checking use of S3 registration ... -√  checking use of S3 registration (1.9s)
   checking dependencies in R code ...
   checking dependencies in R code ... 
√  checking dependencies in R code (2.3s)
   checking S3 generic/method consistency ...
   checking S3 generic/method consistency ... 
√  checking S3 generic/method consistency (2.5s)
   checking replacement functions ...
   checking replacement functions ... -√  checking replacement functions (1.5s)
   checking foreign function calls ...
   checking foreign function calls ... -√  checking foreign function calls (1.7s)
   checking R code for possible problems ...
   checking R code for possible problems ... 
√  checking R code for possible problems (11.2s)
   checking Rd files ...
   checking Rd files ... -√  checking Rd files
   checking Rd metadata ...
   checking Rd metadata ... -√  checking Rd metadata
   checking Rd line widths ...
   checking Rd line widths ... 
√  checking Rd line widths
   checking Rd cross-references ...
   checking Rd cross-references ... -√  checking Rd cross-references
   checking for missing documentation entries ...
   checking for missing documentation entries ... -√  checking for missing documentation entries (1.7s)
   checking for code/documentation mismatches ...
   checking for code/documentation mismatches ... -√  checking for code/documentation mismatches (4.6s)
   checking Rd \usage sections ...
   checking Rd \usage sections ... 
√  checking Rd \usage sections (2.8s)
   checking Rd contents ...
   checking Rd contents ... -√  checking Rd contents
   checking for unstated dependencies in examples ...
   checking for unstated dependencies in examples ... -√  checking for unstated dependencies in examples (525ms)
   checking contents of 'data' directory ...
√  checking contents of 'data' directory
   checking data for non-ASCII characters ...
   checking data for non-ASCII characters ... -√  checking data for non-ASCII characters (340ms)
   checking data for ASCII and uncompressed saves ...
   checking data for ASCII and uncompressed saves ... 
√  checking data for ASCII and uncompressed saves (351ms)-  
   checking installed files from 'inst/doc' ...-   checking installed files from 'inst/doc' ... 
√  checking installed files from 'inst/doc'
   checking files in 'vignettes' ...-   checking files in 'vignettes' ... 
√  checking files in 'vignettes'
   checking examples ...
   checking examples ... -N  checking examples (1h 27m 17s)
   Examples with CPU or elapsed time > 5s
                             user system elapsed
   doRun                  4261.83   0.50 4263.99
   boxcoxTransformation    596.23   0.41  597.33
   TreEvo-package          294.91   0.06  295.27
   methodsPLS               52.86   0.00   52.86
   landscapeFPK_Intrinsic   10.46   0.00   10.49-   
   landscapeFPK_Intrinsic   10.46   0.00   10.49
   checking for unstated dependencies in 'tests' ...
   checking for unstated dependencies in 'tests' ... 
√  checking for unstated dependencies in 'tests'
   checking tests ...
     checking tests ...
     Running 'testthat.R'
-  -  
√  Running 'testthat.R' [238s]-  
   checking for unstated dependencies in vignettes ...
   checking for unstated dependencies in vignettes ... 
√  checking for unstated dependencies in vignettes (555ms)
   checking package vignettes in 'inst/doc' ...
   checking package vignettes in 'inst/doc' ... -√  checking package vignettes in 'inst/doc'
   checking re-building of vignette outputs ...
   checking re-building of vignette outputs ... 
√  checking re-building of vignette outputs (3.1s)
   checking PDF version of manual ...
   checking PDF version of manual ... 
√  checking PDF version of manual (10.4s)-
   See
     'C:/Users/dwbapst/AppData/Local/Temp/RtmpEBgWZV/TreEvo.Rcheck/00check.log'
   for details.
-

-- R CMD check results -------------------------------------- TreEvo 0.20.3 ----
Duration: 1h 33m 55.4s
> checking CRAN incoming feasibility ... NOTE
  Maintainer: 'David Bapst <dwbapst@gmail.com>'
  New submission
> checking package dependencies ... NOTE
  Packages suggested but not available for checking: 'doMC' 'gpclib'
> checking examples ... NOTE
  Examples with CPU or elapsed time > 5s
                            user system elapsed
  doRun                  4261.83   0.50 4263.99
  boxcoxTransformation    596.23   0.41  597.33
  TreEvo-package          294.91   0.06  295.27
  methodsPLS               52.86   0.00   52.86
  landscapeFPK_Intrinsic   10.46   0.00   10.49
0 errors √ | 0 warnings √ | 3 notes x
>