[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
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