[Bioc-devel] weird unit test error

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Jan 7 01:32:47 CET 2020


The error is reproducible for me

> devtools::test(filter="examples")
Loading animalcules
Registered S3 method overwritten by 'xts':
  method     from
  as.zoo.xts zoo
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo
Testing animalcules
✔ |  OK F W S | Context
✖ |  38 1     | examples [33.1 s]
────────────────────────────────────────────────────────────────────────────────
test-examples.R:87: failure: do_alpha_div_test() is working
`pval_t` not equal to 0.49.
1/1 mismatches
[1] 0.37 - 0.49 == -0.12
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 33.2 s

OK:       38
Failed:   1
Warnings: 0
Skipped:  0
>

When run under R-devel

> sessionInfo()
R Under development (unstable) (2019-12-27 r77623)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-devel/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-devel/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] DMwR_0.4.1        caret_6.0-84      ggplot2_3.2.1     lattice_0.20-38
[5] animalcules_1.3.2 testthat_2.3.1

loaded via a namespace (and not attached):
  [1] backports_1.1.5             plyr_1.8.5
  [3] lazyeval_0.2.2              splines_4.0.0
  [5] crosstalk_1.0.0             BiocParallel_1.21.2
  [7] usethis_1.5.1.9000          GenomeInfoDb_1.23.1
  [9] digest_0.6.23               foreach_1.4.7
 [11] htmltools_0.4.0             gdata_2.18.0
 [13] fansi_0.4.0                 magrittr_1.5
 [15] memoise_1.1.0               covr_3.4.0
 [17] cluster_2.1.0               ROCR_1.0-7
 [19] limma_3.43.0                remotes_2.1.0
 [21] recipes_0.1.8               annotate_1.65.0
 [23] gower_0.2.1                 matrixStats_0.55.0
 [25] xts_0.11-2                  prettyunits_1.0.2
 [27] colorspace_1.4-1            blob_1.2.0
 [29] dplyr_0.8.3                 callr_3.4.0
 [31] crayon_1.3.4                RCurl_1.95-4.12
 [33] jsonlite_1.6                genefilter_1.69.0
 [35] zeallot_0.1.0               survival_3.1-8
 [37] zoo_1.8-6                   iterators_1.0.12
 [39] ape_5.3                     glue_1.3.1
 [41] gtable_0.3.0                ipred_0.9-9
 [43] zlibbioc_1.33.0             XVector_0.27.0
 [45] DelayedArray_0.13.1         pkgbuild_1.0.6
 [47] Rhdf5lib_1.9.0              shape_1.4.4
 [49] BiocGenerics_0.33.0         quantmod_0.4-15
 [51] rentrez_1.2.2               abind_1.4-5
 [53] scales_1.1.0                DBI_1.1.0
 [55] Rcpp_1.0.3                  plotROC_2.2.1
 [57] viridisLite_0.3.0           xtable_1.8-4
 [59] bit_1.1-14                  DT_0.11
 [61] stats4_4.0.0                tsne_0.1-3
 [63] lava_1.6.6                  prodlim_2019.11.13
 [65] glmnet_3.0-2                htmlwidgets_1.5.1
 [67] rex_1.1.2                   httr_1.4.1
 [69] gplots_3.0.1.1              RColorBrewer_1.1-2
 [71] ellipsis_0.3.0              farver_2.0.1
 [73] pkgconfig_2.0.3             XML_3.98-1.20
 [75] nnet_7.3-12                 locfit_1.5-9.1
 [77] labeling_0.3                tidyselect_0.2.5
 [79] rlang_0.4.2                 reshape2_1.4.3
 [81] later_1.0.0                 AnnotationDbi_1.49.0
 [83] munsell_0.5.0               tools_4.0.0
 [85] cli_2.0.0                   generics_0.0.2
 [87] RSQLite_2.1.5               devtools_2.2.1
 [89] biomformat_1.15.0           stringr_1.4.0
 [91] fastmap_1.0.1               ModelMetrics_1.2.2
 [93] processx_3.4.1              bit64_0.9-7
 [95] fs_1.3.1                    caTools_1.17.1.3
 [97] purrr_0.3.3                 nlme_3.1-143
 [99] mime_0.8                    compiler_4.0.0
[101] rstudioapi_0.10             curl_4.3
[103] plotly_4.9.1                tibble_2.1.3
[105] geneplotter_1.65.0          stringi_1.4.3
[107] ps_1.3.0                    desc_1.2.0
[109] forcats_0.4.0               Matrix_1.2-18
[111] shinyjs_1.0                 vegan_2.5-6
[113] permute_0.9-5               vctrs_0.2.1
[115] pillar_1.4.3                lifecycle_0.1.0
[117] data.table_1.12.8           bitops_1.0-6
[119] httpuv_1.5.2                GenomicRanges_1.39.1
[121] R6_2.4.1                    promises_1.1.0
[123] KernSmooth_2.23-16          IRanges_2.21.2
[125] sessioninfo_1.1.1           codetools_0.2-16
[127] gtools_3.8.1                MASS_7.3-51.5
[129] assertthat_0.2.1            pkgload_1.0.2
[131] rhdf5_2.31.1                SummarizedExperiment_1.17.1
[133] DESeq2_1.27.18              rprojroot_1.3-2
[135] withr_2.1.2                 S4Vectors_0.25.8
[137] GenomeInfoDbData_1.2.2      mgcv_1.8-31
[139] parallel_4.0.0              MultiAssayExperiment_1.13.4
[141] rpart_4.1-15                timeDate_3043.102
[143] tidyr_1.0.0                 class_7.3-15
[145] TTR_0.23-6                  Biobase_2.47.2
[147] shiny_1.4.0                 lubridate_1.7.4

So it does not seem 'weird'. Are you testing your package locally under R-devel, which is the version currently in use for the devel branch of Bioconductor?

Martin

On 1/7/20, 1:26 AM, "Bioc-devel on behalf of Yue Zhao (Jason)" <bioc-devel-bounces using r-project.org on behalf of yuezh using bu.edu> wrote:

    Hello developers,
    
    Recently I got an error in the devel-branch test:
    http://bioconductor.org/checkResults/devel/bioc-LATEST/animalcules/malbec2-checksrc.html
    
    It works just fine in the current bioc version, and the error says:
    "non-numeric argument to mathematical function" to this command:
    round(p$`Wilcoxon rank sum test`, 2)
    
    Does anyone have similar issues in the devel branch? Thanks!
    
    Best,
    Jason
    
    
    *--*
    
    *Yue (Jason) Zhao*
    
    PhD Candidate, Bioinformatics Program
    
    Boston University
    
    yuezh using bu.edu
    
    	[[alternative HTML version deleted]]
    
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