CRAN Package Check Results for Package poppr

Last updated on 2015-09-06 23:47:35.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.2 7.60 124.09 131.68 OK
r-devel-linux-x86_64-debian-gcc 2.0.2 7.77 122.94 130.72 OK
r-devel-linux-x86_64-fedora-clang 2.0.2 242.85 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.2 222.91 NOTE
r-devel-osx-x86_64-clang 2.0.2 231.69 OK
r-devel-windows-ix86+x86_64 2.0.2 32.00 395.00 427.00 OK
r-patched-linux-x86_64 2.0.2 8.32 130.38 138.70 OK
r-patched-solaris-sparc 2.0.2 1545.40 ERROR
r-patched-solaris-x86 2.0.2 370.40 OK
r-release-linux-x86_64 2.0.2 8.18 128.65 136.84 OK
r-release-osx-x86_64-mavericks 2.0.2 OK
r-release-windows-ix86+x86_64 2.0.2 49.00 253.00 302.00 OK
r-oldrel-windows-ix86+x86_64 2.0.2 57.00 373.00 430.00 OK

Memtest notes: valgrind

Check Details

Version: 2.0.2
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: adegenet
    Loading required package: ade4
    
     /// adegenet 2.0.0 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature resquests: adegenetIssues()
    
    
    This is poppr version 2.0.2. To get started, type package?poppr
    OMP parallel support: available
    Loading required package: ape
    Error : cannot evaluate distance function, it might be missing.
    pandoc-citeproc:
    Error at "source" (line 1, column 1380):
    unexpected end of input
    expecting new-line
    The association of alleles among different loci was studied in natural populations of Hordeum spontaneum, the evolutionary progenitor of cultivated barley. The variance of the number of heterozygous loci in two randomly chosen gametes affords a useful measure of such association. The behavior of this statistic in several particular models is described. Generally, linkage (gametic phase) disequilibrium tends to increase the variance above the value expected under complete independence. This increase is greatest when disequilibria are such as to maximize the sum of squares of the two-locus gametic frequencies.—When data on several loci per individual are available, the observed variance may be tested for its agreement with that expected under the hypothesis of complete interlocus independence, using the sampling theory of this model. When applied to allozyme data from 26 polymorphic populations of wild barley, this test demonstrated the presence of geographically widespread multilocus organization. On average, the variance was 80% higher than expected under random association. Gametic frequencies for four esterase loci in both of these populations of wild barley and two composite crosses of cultivated barley were analyzed. Most generations of the composites showed less multilocus structure, as measured by the indices of association, than the wild populations.
     ^
    pandoc: Error running filter /usr/bin/pandoc-citeproc
    Error: processing vignette 'mlg.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 83
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0.2
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: adegenet
    Loading required package: ade4
    
     /// adegenet 2.0.0 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature resquests: adegenetIssues()
    
    
    This is poppr version 2.0.2. To get started, type package?poppr
    OMP parallel support: available
    Loading required package: ape
    Quitting from lines 255-263 (mlg.Rmd)
    Error: processing vignette 'mlg.Rmd' failed with diagnostics:
    invalid grey level, must be in [0,1]
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.0.2
Check: examples
Result: ERROR
    Running examples in ‘poppr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: bitwise.dist
    > ### Title: Calculate a distance matrix comparing samples based on the
    > ### number of alleles that differ in zygosity.
    > ### Aliases: bitwise.dist
    >
    > ### ** Examples
    >
    > set.seed(999)
    > x <- glSim(n.ind = 10, n.snp.nonstruc = 5e2, n.snp.struc = 5e2, ploidy = 2)
    
     *** caught segfault ***
    address a800000, cause 'memory not mapped'
Flavor: r-patched-solaris-sparc

Version: 2.0.2
Check: tests
Result: ERROR
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
    
     /// adegenet 2.0.0 is loaded ////////////
    
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()'
     > bug reports/feature resquests: adegenetIssues()
    
    
     This is poppr version 2.0.2. To get started, type package?poppr
     OMP parallel support: available
    
     *** caught segfault ***
     address 8, cause 'memory not mapped'
Flavor: r-patched-solaris-sparc