Comments (10)
zkamvar
commented on September 26, 2024
I think rather, I will fix the issue in mlg.table and call unclass before I return it.
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zkamvar
commented on September 26, 2024
I will add a new tag once this has been accepted into CRAN.
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zkamvar
commented on September 26, 2024
This apparently is still breaking on Windows devel.
R Under development (unstable) (2015-05-10 r68348) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> test_check("poppr")
Loading required package: poppr
Loading required package: adegenet
Loading required package: ade4
==========================
adegenet 1.4-2 is loaded
==========================
- to start, type '?adegenet'
- to browse adegenet website, type 'adegenetWeb()'
- to post questions/comments: adegenet-forum@lists.r-forge.r-project.org
This is poppr version 1.1.4. To get started, type package?poppr
Amova tests : 12
Graph color conversion tests : ...
Population Distance Tests : ......
Genclone coercion tests : ...................
Greyscale tests : ...
Data import tests : ..
Missing tests : ......
Multilocus genotype tests : ...............3..........
Polyploid Tests : ....
Poppr table tests : ......................
Population subset tests : ..................................
Analytical value tests : ............
1. Error: Amova returns published values ---------------------------------------
missing value where TRUE/FALSE needed
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr.amova(Aeut, ~Pop/Subpop, quiet = TRUE) at test-amova.R:5
5: ade4::amova(samples = xtab, distances = xdist, structures = xstruct)
2. Error: AMOVA handles subsetted genclone objects -----------------------------
missing value where TRUE/FALSE needed
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: poppr.amova(Athena, ~Subpop, quiet = TRUE) at test-amova.R:30
5: ade4::amova(samples = xtab, distances = xdist, structures = xstruct)
3. Failure(@test-mlg.R#50): mlg.crosspop will work with subsetted genclone objects
x <- mlg.crosspop(Athena, quiet = TRUE) not equal to expected_output
Component "MLG.13": Attributes: < names for current but not for target >
Component "MLG.13": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.13": target is numeric, current is table
Component "MLG.23": Attributes: < names for current but not for target >
Component "MLG.23": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.23": target is numeric, current is table
Component "MLG.24": Attributes: < names for current but not for target >
Component "MLG.24": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.24": target is numeric, current is table
Component "MLG.32": Attributes: < names for current but not for target >
Component "MLG.32": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.32": target is numeric, current is table
Component "MLG.52": Attributes: < names for current but not for target >
Component "MLG.52": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.52": target is numeric, current is table
Component "MLG.63": Attributes: < names for current but not for target >
Component "MLG.63": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.63": target is numeric, current is table
Error: Test failures
In addition: Warning messages:
1: In Ops.factor(left, right) : '<' not meaningful for factors
2: In Ops.factor(left, right) : '<' not meaningful for factors
3: In Ops.factor(left, right) : '<' not meaningful for factors
4: In Ops.factor(left, right) : '<' not meaningful for factors
Execution haltedfrom poppr.
zkamvar
commented on September 26, 2024
This might not be an issue. The report above clearly states poppr version 1.1.4, whereas I had submitted version 1.1.5.
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zkamvar
commented on September 26, 2024
For posterity:
[This was generated from CRAN.R-project.org/submit.html]
The following package was uploaded to CRAN:
===========================================
Package Information:
Package: poppr
Version: 1.1.5
Title: Genetic Analysis of Populations with Mixed Reproduction
Author(s): Zhian N. Kamvar [cre, aut], Javier F. Tabima [aut], Niklaus J.
Grunwald [ths]
Maintainer: Zhian N. Kamvar <[email protected]>
Depends: R (>= 2.15.1), adegenet (>= 1.4-2)
Suggests: testthat, knitr, polysat
Description: Population genetic analyses for hierarchical analysis of
partially clonal populations built upon the architecture of
the 'adegenet' package.
License: GPL-2 | GPL-3
Imports: vegan, ggplot2, phangorn, ape (>= 3.1-1), igraph, methods,
ade4, pegas, reshape2
The maintainer confirms that he or she
has read and agrees to the CRAN policies.
Submitter's comment: This fix addresses three issues:
1. A change in
behavior for [.table in R-devel that affected poppr's
mlg.table
2. Title case in DESCRIPTION
3. single
quote 'adegenet' in DESCRIPTION
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zkamvar
commented on September 26, 2024
NOPE:
R Under development (unstable) (2015-05-10 r68348) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> test_check("poppr")
Loading required package: poppr
Loading required package: adegenet
Loading required package: ade4
==========================
adegenet 1.4-2 is loaded
==========================
- to start, type '?adegenet'
- to browse adegenet website, type 'adegenetWeb()'
- to post questions/comments: adegenet-forum@lists.r-forge.r-project.org
This is poppr version 1.1.5. To get started, type package?poppr
1. Failure (@test-mlg.R#50): mlg.crosspop will work with subsetted genclone objects
x <- mlg.crosspop(Athena, quiet = TRUE) not equal to expected_output
Component "MLG.13": Attributes: < names for current but not for target >
Component "MLG.13": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.13": target is numeric, current is table
Component "MLG.23": Attributes: < names for current but not for target >
Component "MLG.23": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.23": target is numeric, current is table
Component "MLG.24": Attributes: < names for current but not for target >
Component "MLG.24": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.24": target is numeric, current is table
Component "MLG.32": Attributes: < names for current but not for target >
Component "MLG.32": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.32": target is numeric, current is table
Component "MLG.52": Attributes: < names for current but not for target >
Component "MLG.52": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.52": target is numeric, current is table
Component "MLG.63": Attributes: < names for current but not for target >
Component "MLG.63": Attributes: < Length mismatch: comparison on first 0 components >
Component "MLG.63": target is numeric, current is table
testthat results ================================================================
OK: 143 SKIPPED: 0 FAILED: 1
1. Failure (@test-mlg.R#50): mlg.crosspop will work with subsetted genclone objects
Error: testthat unit tests failed
Execution haltedfrom poppr.
zkamvar
commented on September 26, 2024
Link: http://win-builder.r-project.org/ji5j9eob8k4n/
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zkamvar
commented on September 26, 2024
Fixed as of 82eb32d
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zkamvar
commented on September 26, 2024
Once again, I will send up a new version once mother CRAN has accepted it.
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zkamvar
commented on September 26, 2024
by which I mean add a tag
from poppr.
Related Issues (20)
- Fix inefficient implementation of boot.bruvo HOT 3
- Interpretation of negative values in AMOVA HOT 3
- Error with reverse dependency checks for phangorn HOT 12
- genind2genalex() produces all zero genotypes with some SNP data. HOT 1
- bitwise.ia() degraded performance on windows HOT 1
- Clade rooting abnormally with updated HOT 4
- Error in bruvo.boot HOT 4
- CRAN test failure in R-devel on Debian
- Cannot re-level strata of a snpclone object HOT 1
- DUE 2021-09-21: Packages including omp.h after Rincludes.h
- Feature request: separation/removal of sf package requirement HOT 5
- Optional disabling of statistics in poppr table HOT 6
- threads not being respected and defaulting to 1 HOT 1
- PAIRWISE FST Calculation HOT 1
- Find All Duplicate MLGs HOT 4
- [read.genalex()]: Detect semicolon-separated files and throw error with correct command
- IS there a way to make a table indicated the multilocus genotypes for each isolate? where is that info stored? HOT 1
- Error Message from R using read.genalex HOT 1
- CRAN Errors to fix by 2023-03-22 HOT 2
- Preserve state of random number generator in .onAttach() HOT 6
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