CRAN Package Check Results for Package cytominer

Last updated on 2018-08-21 16:50:19 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.0 1.68 186.59 188.27 OK
r-devel-linux-x86_64-debian-gcc 0.1.0 1.52 141.39 142.91 OK
r-devel-linux-x86_64-fedora-clang 0.1.0 203.31 OK
r-devel-linux-x86_64-fedora-gcc 0.1.0 210.69 OK
r-devel-windows-ix86+x86_64 0.1.0 7.00 70.00 77.00 ERROR
r-patched-linux-x86_64 0.1.0 1.60 181.47 183.07 ERROR
r-patched-solaris-x86 0.1.0 265.10 OK
r-release-linux-x86_64 0.1.0 1.52 179.35 180.87 NOTE
r-release-windows-ix86+x86_64 0.1.0 8.00 63.00 71.00 OK
r-release-osx-x86_64 0.1.0 OK
r-oldrel-windows-ix86+x86_64 0.1.0 3.00 66.00 69.00 OK
r-oldrel-osx-x86_64 0.1.0 OK

Check Details

Version: 0.1.0
Check: examples
Result: ERROR
    Running examples in 'cytominer-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: replicate_correlation
    > ### Title: Measure replicate correlation of variables.
    > ### Aliases: replicate_correlation
    >
    > ### ** Examples
    >
    > set.seed(123)
    > x1 <- rnorm(10)
    > x2 <- x1 + rnorm(10) / 100
    > y1 <- rnorm(10)
    > y2 <- y1 + rnorm(10) / 10
    > z1 <- rnorm(10)
    > z2 <- z1 + rnorm(10) / 1
    >
    > batch <- rep(rep(1:2, each=5), 2)
    >
    > treatment <- rep(1:10, 2)
    >
    > replicate_id <- rep(1:2, each=10)
    >
    > sample <-
    + tibble::data_frame(x = c(x1, x2), y = c(y1, y2), z = c(z1, z2),
    + Metadata_treatment = treatment,
    + Metadata_replicate_id = replicate_id,
    + Metadata_batch = batch)
    >
    > head(sample)
    # A tibble: 6 x 6
     x y z Metadata_treatment Metadata_replicate_id Metadata_batch
     <dbl> <dbl> <dbl> <int> <int> <int>
    1 -0.560 -1.07 -0.695 1 1 1
    2 -0.230 -0.218 -0.208 2 1 1
    3 1.56 -1.03 -1.27 3 1 1
    4 0.0705 -0.729 2.17 4 1 1
    5 0.129 -0.625 1.21 5 1 1
    6 1.72 -1.69 -1.12 6 1 2
    >
    > # `replicate_correlation`` returns the median, min, and max
    > # replicate correlation (across batches) per variable
    > replicate_correlation(sample = sample,
    + variables = c("x", "y", "z"),
    + strata = c("Metadata_treatment"),
    + replicates = 2,
    + split_by = "Metadata_batch",
    + replicate_by = "Metadata_replicate_id",
    + cores = 1)
    # A tibble: 3 x 4
     variable median min max
     <chr> <dbl> <dbl> <dbl>
    1 x 1.000 1.000 1.000
    2 y 0.996 0.993 0.999
    3 z 0.627 0.290 0.964
    >
    >
    >
    >
    > cleanEx()
    Error: connections left open:
     <-CRANwin.fb05.statistik.uni-dortmund.de:11807 (sockconn)
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.1.0
Check: DESCRIPTION meta-information
Result: NOTE
    Dependence on R version ‘3.3.3’ not with patchlevel 0
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [143s/153s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > Sys.setenv("R_TESTS" = "")
     >
     > library(testthat)
     > library(cytominer)
    
     Attaching package: 'cytominer'
    
     The following object is masked from 'package:stats':
    
     aggregate
    
     The following object is masked from 'package:base':
    
     transform
    
     >
     > test_check("cytominer")
     ── 1. Failure: `replicate_correlation` measures correlationbetween replicates in
     `%>%`(...) not equal to correlations %>% as.data.frame().
     Attributes: < Component "row.names": Numeric: lengths (1, 3) differ >
     Component "variable": Lengths (1, 3) differ (string compare on first 1)
     Component "variable": 1 string mismatch
     Component "median": Numeric: lengths (1, 3) differ
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 232 SKIPPED: 0 FAILED: 1
     1. Failure: `replicate_correlation` measures correlationbetween replicates in each feature (@test-replicate_correlation.R#71)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64