[Bioc-devel] Strange error with function existing in the collated R files

[Hervé Pagès]

Hi Panagiotis,

Make sure to keep your installation up-to-date by running 
BiocManager::install() frequently.

Also check that you have a valid installation with BiocManager::valid().

Then you should be able to reproduce locally with:

   library(recoup)
   example(mergeRuns)

That reproduces the error for me on my laptop. See my sessionInfo() below.

Best,

H.

 > sessionInfo()
R Under development (unstable) (2022-03-24 r81969)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.2.r81969/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.2.r81969/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB              LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils datasets
[8] methods   base

other attached packages:
  [1] recoup_1.23.2               ComplexHeatmap_2.11.1
  [3] ggplot2_3.3.5               GenomicAlignments_1.31.2
  [5] Rsamtools_2.11.0            Biostrings_2.63.3
  [7] XVector_0.35.0              SummarizedExperiment_1.25.3
  [9] Biobase_2.55.2              MatrixGenerics_1.7.0
[11] matrixStats_0.62.0          GenomicRanges_1.47.6
[13] GenomeInfoDb_1.31.7         IRanges_2.29.1
[15] S4Vectors_0.33.17           BiocGenerics_0.41.2

loaded via a namespace (and not attached):
  [1] bitops_1.0-7            bit64_4.0.5 filelock_1.0.2
  [4] doParallel_1.0.17       RColorBrewer_1.1-3 progress_1.2.2
  [7] httr_1.4.2              tools_4.2.0 utf8_1.2.2
[10] R6_2.5.1                DBI_1.1.2 colorspace_2.0-3
[13] GetoptLong_1.0.5        withr_2.5.0 tidyselect_1.1.2
[16] prettyunits_1.1.1       bit_4.0.4 curl_4.3.2
[19] compiler_4.2.0          cli_3.2.0 xml2_1.3.3
[22] DelayedArray_0.21.2     labeling_0.4.2 rtracklayer_1.55.4
[25] scales_1.2.0            rappdirs_0.3.3 stringr_1.4.0
[28] digest_0.6.29           pkgconfig_2.0.3 dbplyr_2.1.1
[31] fastmap_1.1.0           rlang_1.0.2 GlobalOptions_0.1.2
[34] RSQLite_2.2.12          farver_2.1.0 shape_1.4.6
[37] BiocIO_1.5.0            generics_0.1.2 BiocParallel_1.29.21
[40] dplyr_1.0.8             RCurl_1.98-1.6 magrittr_2.0.3
[43] GenomeInfoDbData_1.2.8  Matrix_1.4-1 Rcpp_1.0.8.3
[46] munsell_0.5.0           fansi_1.0.3 lifecycle_1.0.1
[49] yaml_2.3.5              stringi_1.7.6 zlibbioc_1.41.0
[52] BiocFileCache_2.3.4     blob_1.2.3 parallel_4.2.0
[55] crayon_1.5.1            lattice_0.20-45 GenomicFeatures_1.47.14
[58] circlize_0.4.14         hms_1.1.1 KEGGREST_1.35.0
[61] magick_2.7.3            pillar_1.7.0 rjson_0.2.21
[64] codetools_0.2-18        biomaRt_2.51.4 XML_3.99-0.9
[67] glue_1.6.2              png_0.1-7 vctrs_0.4.1
[70] foreach_1.5.2           gtable_0.3.0 purrr_0.3.4
[73] clue_0.3-60             assertthat_0.2.1 cachem_1.0.6
[76] restfulr_0.0.13         tibble_3.1.6 iterators_1.0.14
[79] AnnotationDbi_1.57.1    memoise_2.0.1 cluster_2.1.3
[82] ellipsis_0.3.2


On 20/04/2022 21:16, Panagiotis Moulos wrote:
> Hi all,
>
> I am getting a strange error in the check of my package recoup in the
> current dev branch.
> https://master.bioconductor.org/checkResults/3.15/bioc-LATEST/recoup
>
> It seems that the error is originated by the tests not being able to find a
> function, however this function exists in the collated R files in the
> DESCRIPTION of the package and everything builds and checks locally...
>
> The error:
>
> Error in makeHorizontalAnnotation(width, opts, "heatmap") :
>    could not find function "makeHorizontalAnnotation"
>
> I would really appreciate it if there are any ideas or someone has
> encountered this before.
>
> Thanks.
>
-- 
Hervé Pagès

Bioconductor Core Team
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