New diversity functions
Issue #75
resolved
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Comments (9)
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Thanks, the remaining errors I have involve the tidyeval and testTopology errors. The latter can be fixed with a merge since that is part of Ken’s additions I believe. The tidyeval has to be fixed in the same way Susanna did already which I can handle independently after merging.
* using log directory ‘/home/ruoyi/Dropbox/hg/alakazam.Rcheck’ * using R version 3.4.2 (2017-09-28) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--run-donttest --as-cran’ * checking for file ‘alakazam/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘alakazam’ version ‘0.2.11.999’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Jason Vander Heiden <jason.vanderheiden@yale.edu>’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘alakazam’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calculateAlphaDiversity: no visible binding for global variable ‘.’ calculateAlphaDiversity: no visible binding for global variable ‘D’ calculateAlphaDiversity: no visible binding for global variable ‘D_ERROR’ calculateAlphaDiversity: no visible binding for global variable ‘Q’ calculateAlphaDiversity: no visible binding for global variable ‘D_0’ calculateAlphaDiversity: no visible binding for global variable ‘D_LOWER’ calculateAlphaDiversity: no visible binding for global variable ‘D_UPPER’ calculateBetaDiversity: no visible binding for global variable ‘.’ calculateBetaDiversity: no visible binding for global variable ‘Q’ calculateBetaDiversity: no visible binding for global variable ‘D’ calculateBetaDiversity: no visible binding for global variable ‘D_0’ calculateBetaDiversity: no visible binding for global variable ‘D_LOWER’ calculateBetaDiversity: no visible binding for global variable ‘D_UPPER’ estimateAbundance : bootstrap_: no visible binding for global variable ‘.’ estimateAbundance: no visible binding for global variable ‘SEQUENCES’ estimateAbundance: no visible binding for global variable ‘.’ estimateAbundance: no visible binding for global variable ‘C’ estimateAbundance: no visible binding for global variable ‘P’ estimateAbundance: no visible binding for global variable ‘P_ERROR’ helperBeta: no visible binding for global variable ‘.’ helperBeta: no visible binding for global variable ‘Q’ helperBeta: no visible binding for global variable ‘GAMMA’ helperBeta: no visible binding for global variable ‘ALPHA’ helperBeta: no visible binding for global variable ‘D’ helperBeta: no visible binding for global variable ‘D_ERROR’ helperTest: no visible binding for global variable ‘.’ helperTest: no visible binding for global variable ‘Q’ helperTest: no visible binding for global variable ‘D’ plotDiversityTest: no visible binding for global variable ‘Q’ Undefined global functions or variables: . ALPHA C D D_0 D_ERROR D_LOWER D_UPPER GAMMA P P_ERROR Q SEQUENCES Consider adding importFrom("stats", "C", "D") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NOTE Examples with CPU or elapsed time > 5s user system elapsed plotMRCATest 5.463 0.01 5.519 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs -
Most of the visible binding errors can be fixed by converting the tidyverse calls to standard-evaluation. @ssnn should be able to explain how to do this. It's intially confusing, but ultimately pretty simple to implement. It'll mostly be things like replacing
SEQUENCESwithrlang::sym("SEQUENCES").The one exception is the
.. For this, add. <- NULLto the very top of each function with the error; seecountGenesfor an example.You should fix all these before merging, except for those topology tests if they are indeed fixed in the default branch. That’s pretty much the point of having branches - to have a safe space to make unstable code production ready before merging into the main branch. :)
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Sounds good…attaching the checks below. Getting a warning below however…
WARNING '::' or ':::' import not declared from: ‘rlang’Will merge and hand off to you guys then.
[ruoyi@localhost hg]$ R CMD check --as-cran --run-donttest --timings alakazam_0.2.11.999.tar.gz * using log directory ‘/home/ruoyi/Dropbox/hg/alakazam.Rcheck’ * using R version 3.4.2 (2017-09-28) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--run-donttest --as-cran’ * checking for file ‘alakazam/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘alakazam’ version ‘0.2.11.999’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Jason Vander Heiden <jason.vanderheiden@yale.edu>’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘alakazam’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘rlang’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NOTE Examples with CPU or elapsed time > 5s user system elapsed plotMRCATest 5.533 0 5.569 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE -
Unless you have a typo, that error should vanish after the merge because it's just a missing
@importFromdirective. -
Should add import rlang in DESCRIPTION and import_from rlang sym ayms in <<package>>.R file
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Oh… yep, the same as Jason said
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Ok merged.
rlang still has a WARNING despite merge but not relevant to this issue so closing this.
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Errors to fix before merging the diversity-generalization branch
Build Errors
R CMD check --as-cran --run-donttest --timings
Test Failures