[Bioc-devel] SPB inconsistencies

[Ludwig Geistlinger]

Hi,


According to


http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html


all SPB machines run different snapshots of R-devel with the most recent one (2019-01-22 r76000,

already >1 month outdated) installed on celaya2.


I observe two things:


1. My package builds on celaya2, but fails to build on the other SPB machines running older R-devel snapshots.


http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVRanger/


2. Further, I can't reproduce the SPB built error using a recent R-devel snapshot (2019-02-24 r76155) through the bioconductor/devel_base2 docker container.


Can you please advise on how to best proceed from my side? Just wait for the SPB R-devel being updated?


> sessionInfo()

R Under development (unstable) (2019-02-24 r76155)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
 [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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] TCGAutils_1.3.19
 [2] BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99
 [3] BSgenome.Btaurus.UCSC.bosTau6_1.4.0
 [4] BSgenome_1.51.0
 [5] rtracklayer_1.43.1
 [6] Biostrings_2.51.2
 [7] XVector_0.23.0
 [8] regioneR_1.15.2
 [9] BiocStyle_2.11.0
[10] CNVRanger_0.99.7
[11] curatedTCGAData_1.5.8
[12] edgeR_3.25.3
[13] limma_3.39.12
[14] RaggedExperiment_1.7.4
[15] MultiAssayExperiment_1.9.15
[16] SummarizedExperiment_1.13.0
[17] DelayedArray_0.9.8
[18] BiocParallel_1.17.16
[19] matrixStats_0.54.0
[20] ensembldb_2.7.9
[21] AnnotationFilter_1.7.0
[22] GenomicFeatures_1.35.7
[23] AnnotationDbi_1.45.0
[24] Biobase_2.43.1
[25] GenomicRanges_1.35.1
[26] GenomeInfoDb_1.19.2
[27] IRanges_2.17.4
[28] S4Vectors_0.21.10
[29] AnnotationHub_2.15.7
[30] BiocGenerics_0.29.1

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.15.0           bitops_1.0-6
 [3] bit64_0.9-7                   progress_1.2.0
 [5] httr_1.4.0                    GenomicDataCommons_1.7.3
 [7] tools_3.6.0                   R6_2.4.0
 [9] DBI_1.0.0                     lazyeval_0.2.1
[11] tidyselect_0.2.5              prettyunits_1.0.2
[13] bit_1.1-14                    curl_3.3
[15] compiler_3.6.0                rvest_0.3.2
[17] xml2_1.2.0                    readr_1.3.1
[19] rappdirs_0.3.1                stringr_1.4.0
[21] digest_0.6.18                 Rsamtools_1.99.2
[23] rmarkdown_1.11                pkgconfig_2.0.2
[25] htmltools_0.3.6               rlang_0.3.1
[27] rstudioapi_0.9.0              RSQLite_2.1.1
[29] shiny_1.2.0                   jsonlite_1.6
[31] dplyr_0.8.0.1                 RCurl_1.95-4.11
[33] magrittr_1.5                  GenomeInfoDbData_1.2.0
[35] Matrix_1.2-15                 Rcpp_1.0.0
[37] stringi_1.3.1                 yaml_2.2.0
[39] zlibbioc_1.29.0               grid_3.6.0
[41] blob_1.1.1                    promises_1.0.1
[43] ExperimentHub_1.9.1           crayon_1.3.4
[45] lattice_0.20-38               hms_0.4.2
[47] locfit_1.5-9.1                knitr_1.21
[49] pillar_1.3.1                  biomaRt_2.39.2
[51] XML_3.98-1.17                 glue_1.3.0
[53] evaluate_0.13                 BiocManager_1.30.4
[55] httpuv_1.4.5.1                purrr_0.3.0
[57] assertthat_0.2.0              xfun_0.5
[59] mime_0.6                      xtable_1.8-3
[61] later_0.8.0                   tibble_2.0.1
[63] GenomicAlignments_1.19.1      memoise_1.1.0
[65] interactiveDisplayBase_1.21.0

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