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

Konstantin Okonechnikov k@okonechn|kov @end|ng |rom gm@||@com
Mon Dec 28 13:08:28 CET 2020


I got a note about failing for InTAD package only in Bioc-devel version:

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

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 (
*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,

*R Under development (unstable) (2020-12-26 r79698)Platform:
x86_64-pc-linux-gnu (64-bit)Running under: openSUSE Leap 42.3Matrix
products: defaultBLAS:
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*

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list