Hi Herve, Thanks for your reply!
> Is there a possibility that trena's code is having one worker > downloading/re-installing BSgenome.Hsapiens.UCSC.hg38 while at the same > time another worker is trying to access it? I don’t think any download or reinstalling happens. Several genome packages (hg38, hg19, mm10) are imported by trena as specified in the DESCRIPTION file, and so I assume they must be present after trena is built and installed. Thus - and here’s where I may be confused - there should be nothing to trigger download or re-install as the tests, examples and vignettes are run. In the constructor of the MotifMatcher class, this assignment is made if(genomeName == "hg38"){ reference.genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 } And used later like this: seqs <- as.character(BSgenome::getSeq(obj@reference.genome, gr.regions)) Hence my suggestion that no download or install takes place at run time. In the current design of the unit tests for MotifMatcher, I call the constructor in each test: jaspar.human.pfms <- as.list(query (query(MotifDb, "sapiens"), "jaspar2016")) motifMatcher <- MotifMatcher(genomeName="hg38", pfms=jaspar.human.pfms, quiet=TRUE) For what it’s worth, this code is unchanged in the last year, has run fine on the build system until recently, and passes R CMD check under R3.6.0beta on ubuntu for me. There is no parallelization in this class - but maybe the build system introduces some at a higher level? I can condition these failing tests on hostname in order to pass the build tests if that is not too much of a dodge. - Paul > On Apr 23, 2019, at 12:19 AM, Pages, Herve <hpa...@fredhutch.org> wrote: > > Hi Paul, > > Is there a possibility that trena's code is having one worker > downloading/re-installing BSgenome.Hsapiens.UCSC.hg38 while at the same > time another worker is trying to access it? > > The reason I suspect something like this is that it seems that > BSgenome.Hsapiens.UCSC.hg38 gets reinstalled every night on the builders > and that this happens at the time the build system is running 'R CMD > check' on trena. > > Package vignettes, examples, and unit tests should avoid re-installing > packages. > > H. > > On 4/22/19 15:01, Paul Shannon wrote: >> I cannot reproduce daily build failures found in the trena package by the >> build system. The build report shows: >> >> trena RUnit Tests - 86 test functions, 7 errors, 0 failures >> >> ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library >> operation failed >> ERROR in test_bugInStartEndOfMinusStrandHits: Error in >> .seqlengths_TwoBitFile(x) : UCSC library operation failed >> ERROR in test_findMatchesByChromosomalRegion: Error in >> .seqlengths_TwoBitFile(x) : UCSC library operation failed >> ERROR in test_findMatchesByChromosomalRegion.twoAlternateAlleles: Error in >> .seqlengths_TwoBitFile(x) : UCSC library operation failed >> ERROR in test_findMatchesByMultipleChromosomalRegions: Error in >> .seqlengths_TwoBitFile(x) : UCSC library operation failed >> ERROR in test_getSequence: Error in .seqlengths_TwoBitFile(x) : UCSC library >> operation failed >> ERROR in test_noMatch: Error in .seqlengths_TwoBitFile(x) : UCSC library >> operation failed >> >> This seems similar to a bioc support exchange from two years ago, which may >> suggest that the build system's BSgenome.Hsapiens.UCSC.hg38 is the locus of >> the problem. I offer suggestion very tentatively. >> >> support >> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_95963_&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=1AJWecG5cm0EI_BZG7zYbHNZa3JkQY8pdsJFahrtpIU&s=2WHZQbOLmt-jvKlwVBty43jY5JcBt2U_sdqZDqRxEOY&e= >> >> Any suggestions? >> >> - Paul >> >> sessionInfo() # from my clean R CMD check >> R version 3.6.0 beta (2019-04-11 r76379) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Ubuntu 16.04.5 LTS >> >> Matrix products: default >> BLAS: /local/users/pshannon/src/R-beta/lib/libRblas.so >> LAPACK: /local/users/pshannon/src/R-beta/lib/libRlapack.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=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] stats4 parallel stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] RPostgreSQL_0.6-2 DBI_1.0.0 RUnit_0.4.32 >> [4] trena_1.5.14 MotifDb_1.22.0 Biostrings_2.48.0 >> [7] XVector_0.20.0 IRanges_2.14.12 S4Vectors_0.18.3 >> [10] BiocGenerics_0.26.0 glmnet_2.0-16 foreach_1.4.4 >> [13] Matrix_1.2-17 >> >> loaded via a namespace (and not attached): >> [1] SummarizedExperiment_1.10.1 lassopv_0.2.0 >> [3] progress_1.2.0 lattice_0.20-38 >> [5] rtracklayer_1.40.6 blob_1.1.1 >> [7] XML_3.98-1.19 rlang_0.3.4 >> [9] flare_1.6.0 BiocParallel_1.14.2 >> [11] bit64_0.9-7 splitstackshape_1.4.8 >> [13] matrixStats_0.54.0 GenomeInfoDbData_1.1.0 >> [15] stringr_1.4.0 zlibbioc_1.26.0 >> [17] codetools_0.2-16 memoise_1.1.0 >> [19] Biobase_2.40.0 biomaRt_2.36.1 >> [21] GenomeInfoDb_1.16.0 curl_3.3 >> [23] AnnotationDbi_1.42.1 lars_1.2 >> [25] Rcpp_1.0.1 BSgenome_1.48.0 >> [27] DelayedArray_0.6.6 org.Hs.eg.db_3.6.0 >> [29] bit_1.1-14 Rsamtools_1.32.3 >> [31] BSgenome.Hsapiens.UCSC.hg38_1.4.1 RMySQL_0.10.17 >> [33] hms_0.4.2 digest_0.6.18 >> [35] stringi_1.4.3 GenomicRanges_1.32.7 >> [37] grid_3.6.0 tools_3.6.0 >> [39] bitops_1.0-6 magrittr_1.5 >> [41] RCurl_1.95-4.12 RSQLite_2.1.1 >> [43] randomForest_4.6-14 crayon_1.3.4 >> [45] vbsr_0.0.5 pkgconfig_2.0.2 >> [47] MASS_7.3-51.4 data.table_1.12.2 >> [49] prettyunits_1.0.2 httr_1.4.0 >> [51] assertthat_0.2.1 iterators_1.0.10 >> [53] R6_2.4.0 GenomicAlignments_1.16.0 >> [55] igraph_1.2.4.1 compiler_3.6.0 >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=1AJWecG5cm0EI_BZG7zYbHNZa3JkQY8pdsJFahrtpIU&s=Hd_vdYy62MOejkKAH21haaIJ0HMvjDSH-BxAjBCxSjk&e= > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel