[Bioc-devel] cannot reproduce the build error with InTAD package

[Nitesh Turaga]

Hi Konstantin,

It seems this is a new issue. Please give the devel build machine one more cycle and we'll see if the issue persists. 

Did you try to build it using the command in the build machine log (although I doubt it'll change the end result of successfully building on the bioconductor_docker:devel image) ?

	R CMD build --keep-empty-dirs --no-resave-data InTAD

Best,

Nitesh 

On 12/28/20, 2:07 AM, "Bioc-devel on behalf of Konstantin Okonechnikov" <bioc-devel-bounces using r-project.org on behalf of k.okonechnikov using gmail.com> wrote:

    Hi!

    I got a note about failing for InTAD package only in Bioc-devel version:
    http://bioconductor.org/checkResults/devel/bioc-LATEST/InTAD/machv2-buildsrc.html

    Notably, there were no changes to the package before this error started
    occurring thus I suppose it might be connected to some updates in other
    packages.

    To reproduce the issue I installed the latest available R-devel version and
    also switched to bioconductor-devel. Installing the package worked OK.

    Error message from report was the following:

    Quitting from lines 93-94 (InTAD.Rmd)
    Error: processing vignette 'InTAD.Rmd' failed with diagnostics:
    missing value where TRUE/FALSE needed
    --- failed re-building ‘InTAD.Rmd’

    The problem seems to be occurring in creating the object (
    https://github.com/kokonech/InTAD/blob/master/vignettes/InTAD.Rmd
    ):
    *inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel,mbAnnData)*

    However, I did not observe any issues in package installation. Moreover, I
    managed to build the vignette without problems simply running the following
    command from latest source:

    *rmarkdown::render('InTAD/vignettes/InTAD.Rmd') *

    Any suggestions how I could reproduce and fix this error?  Below I also
    included my sessionInfo()

    Best regards,
       Konstantin




















































    *R Under development (unstable) (2020-12-26 r79698)Platform:
    x86_64-pc-linux-gnu (64-bit)Running under: openSUSE Leap 42.3Matrix
    products: defaultBLAS:
    /home/okonechn/B080/okonechn/tools/R-devel/lib/libRblas.soLAPACK:
    /home/okonechn/B080/okonechn/tools/R-devel/lib/libRlapack.solocale:[1]
    Cattached base packages:[1] parallel  stats4    stats     graphics
     grDevices utils     datasets[8] methods   baseother attached packages: [1]
    BiocStyle_2.19.1            InTAD_1.11.0 [3] MultiAssayExperiment_1.17.2
    SummarizedExperiment_1.21.1 [5] Biobase_2.51.0
     MatrixGenerics_1.3.0 [7] matrixStats_0.57.0
     GenomicRanges_1.43.1 [9] GenomeInfoDb_1.27.3         IRanges_2.25.6[11]
    S4Vectors_0.29.6            BiocGenerics_0.37.0loaded via a namespace (and
    not attached): [1] tidyr_1.1.2              splines_4.1.0
     carData_3.0-4 [4] BiocManager_1.30.10      GenomeInfoDbData_1.2.4
    cellranger_1.1.0 [7] Rsamtools_2.7.0          yaml_2.2.1
    pillar_1.4.7[10] backports_1.2.1          lattice_0.20-41
     glue_1.4.2[13] digest_0.6.27            ggsignif_0.6.0
    XVector_0.31.1[16] qvalue_2.23.0            colorspace_2.0-0
    htmltools_0.5.0[19] Matrix_1.3-0             plyr_1.8.6
    XML_3.99-0.5[22] pkgconfig_2.0.3          broom_0.7.3
     haven_2.3.1[25] bookdown_0.21            zlibbioc_1.37.0
     purrr_0.3.4[28] scales_1.1.1             openxlsx_4.2.3
    rio_0.5.16[31] BiocParallel_1.25.2      tibble_3.0.4
    farver_2.0.3[34] generics_0.1.0           car_3.0-10
    ggplot2_3.3.2[37] ellipsis_0.3.1           ggpubr_0.4.0
    magrittr_2.0.1[40] crayon_1.3.4             readxl_1.3.1
    mclust_5.4.7[43] evaluate_0.14            rstatix_0.6.0
     forcats_0.5.0[46] foreign_0.8-81           tools_4.1.0
     data.table_1.13.4[49] hms_0.5.3                BiocIO_1.1.2
    lifecycle_0.2.0[52] stringr_1.4.0            munsell_0.5.0
     zip_2.1.1[55] DelayedArray_0.17.7      Biostrings_2.59.2
     compiler_4.1.0[58] rlang_0.4.9              grid_4.1.0
    RCurl_1.98-1.2[61] rjson_0.2.20             labeling_0.4.2
    rmarkdown_2.6[64] bitops_1.0-6             restfulr_0.0.13
     gtable_0.3.0[67] abind_1.4-5              curl_4.3
    reshape2_1.4.4[70] R6_2.5.0                 GenomicAlignments_1.27.2
    knitr_1.30[73] dplyr_1.0.2              rtracklayer_1.51.2
    stringi_1.5.3[76] Rcpp_1.0.5               vctrs_0.3.6
     xfun_0.19[79] tidyselect_1.1.0*

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