Thanks for your help. This just showed up last night. I will wait few more days and see if it continues to be an issue. Also, I’ll add pander
- Gabriel On 10/11/18, 7:01 PM, "Hervé Pagès" <hpa...@fredhutch.org> wrote: >Hi Gabriel, > >I'm not able to reproduce this either. See my sessionInfo() >at the end (obtained after running all the code in the >variancePartition.Rnw vignette). > >Did this error just appear today or yesterday, so would follow >your last commit to the RELEASE_3_7 branch? Or did it appear >before e.g. a few days ago? > >If the former, then let's wait a couple more day and see if >the error reproduces. Could be a build machine hiccup and maybe >it will just go away. > >If the latter, then it could be related to the new version of >doParallel (1.0.14) that showed up on CRAN on Sept 24 (18 days >ago). Our build machines picked it up and installed it so now >all builds are using this new version (as you can see by clicking >on the links in the rightmost column of the small table at the >top of the build report). > >As a side note: you use pander in the vignette so would need to >add it to the Suggests field of the package. > >Cheers, >H. > > > sessionInfo() >R version 3.5.1 (2018-07-02) >Platform: x86_64-pc-linux-gnu (64-bit) >Running under: Ubuntu 16.04.5 LTS > >Matrix products: default >BLAS: >/home/hpages/R/R-3.5.1/lib/https://urldefense.proofpoint.com/v2/url?u=http >-3A__libRblas.so&d=DwIFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=KdYcmw5SdXylMrTGSuNVk >NJulowod64k0PTDC5BHZkk&m=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E&s=3jM >Ia0up64DNhDmFncfoVMDawXZIKv8OCyswMc8VWQ0&e= >LAPACK: >/home/hpages/R/R-3.5.1/lib/https://urldefense.proofpoint.com/v2/url?u=http >-3A__libRlapack.so&d=DwIFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=KdYcmw5SdXylMrTGSuN >VkNJulowod64k0PTDC5BHZkk&m=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E&s=M >8hFMwj_eBOoEvdwmXC3h7J_VmhrPPNwg5B7giSrSSs&e= > >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] dendextend_1.8.0 ballgown_2.12.0 > [3] DESeq2_1.20.0 SummarizedExperiment_1.10.1 > [5] DelayedArray_0.6.6 BiocParallel_1.14.2 > [7] matrixStats_0.54.0 GenomicRanges_1.32.7 > [9] GenomeInfoDb_1.16.0 IRanges_2.14.12 >[11] S4Vectors_0.18.3 edgeR_3.22.5 >[13] lme4_1.1-18-1 Matrix_1.2-14 >[15] doParallel_1.0.14 iterators_1.0.10 >[17] variancePartition_1.10.3 Biobase_2.40.0 >[19] BiocGenerics_0.26.0 scales_1.0.0 >[21] foreach_1.4.4 limma_3.36.5 >[23] ggplot2_3.0.0 knitr_1.20 > >loaded via a namespace (and not attached): > [1] minqa_1.2.4 colorspace_1.3-2 class_7.3-14 > > [4] modeltools_0.2-22 colorRamps_2.3 mclust_5.4.1 > > [7] rprojroot_1.3-2 htmlTable_1.12 XVector_0.20.0 > > [10] base64enc_0.1-3 rstudioapi_0.8 flexmix_2.3-14 > > [13] bit64_0.9-7 mvtnorm_1.0-8 >AnnotationDbi_1.42.1 > [16] codetools_0.2-15 splines_3.5.1 >robustbase_0.93-3 > [19] geneplotter_1.58.0 Formula_1.2-3 nloptr_1.2.1 > > [22] Rsamtools_1.32.3 pbkrtest_0.4-7 annotate_1.58.0 > > [25] kernlab_0.9-27 cluster_2.0.7-1 compiler_3.5.1 > > [28] backports_1.1.2 assertthat_0.2.0 lazyeval_0.2.1 > > [31] acepack_1.4.1 htmltools_0.3.6 tools_3.5.1 > > [34] bindrcpp_0.2.2 gtable_0.2.0 glue_1.3.0 > > [37] GenomeInfoDbData_1.1.0 reshape2_1.4.3 dplyr_0.7.6 > > [40] Rcpp_0.12.19 trimcluster_0.1-2.1 >Biostrings_2.48.0 > [43] gdata_2.18.0 nlme_3.1-137 >rtracklayer_1.40.6 > [46] fpc_2.1-11.1 stringr_1.3.1 gtools_3.8.1 > > [49] XML_3.98-1.16 DEoptimR_1.0-8 zlibbioc_1.26.0 > > [52] MASS_7.3-50 BiocStyle_2.8.2 >RColorBrewer_1.1-2 > [55] yaml_2.2.0 memoise_1.1.0 gridExtra_2.3 > > [58] rpart_4.1-13 latticeExtra_0.6-28 stringi_1.2.4 > > [61] RSQLite_2.1.1 genefilter_1.62.0 checkmate_1.8.5 > > [64] >caTools_https://urldefense.proofpoint.com/v2/url?u=http-3A__1.17.1.1&d=DwI >FaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=KdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk >&m=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E&s=c5XRWImsmPTHqu8vDjbP_MZ-k >E4pZylRmN0EZMQIqlA&e= prabclus_2.2-6 rlang_0.2.2 > > [67] pkgconfig_2.0.2 bitops_1.0-6 evaluate_0.12 > > [70] lattice_0.20-35 purrr_0.2.5 bindr_0.1.1 > > [73] GenomicAlignments_1.16.0 htmlwidgets_1.3 labeling_0.3 > > [76] bit_1.1-14 tidyselect_0.2.5 plyr_1.8.4 > > [79] magrittr_1.5 R6_2.3.0 gplots_3.0.1 > > [82] Hmisc_4.1-1 DBI_1.0.0 pillar_1.3.0 > > [85] whisker_0.3-2 foreign_0.8-71 withr_2.1.2 > > [88] mgcv_1.8-24 survival_2.42-6 RCurl_1.95-4.11 > > [91] nnet_7.3-12 tibble_1.4.2 crayon_1.3.4 > > [94] KernSmooth_2.23-15 rmarkdown_1.10 viridis_0.5.1 > > [97] locfit_1.5-9.1 grid_3.5.1 sva_3.28.0 > >[100] data.table_1.11.8 blob_1.1.1 diptest_0.75-7 > >[103] digest_0.6.18 xtable_1.8-3 munsell_0.5.0 > >[106] viridisLite_0.3.0 > > > > >On 10/11/2018 11:38 AM, Hoffman, Gabriel wrote: >> I am the developer of the variancePartition package, and I recently >>made some very small changes to the documentation of my package. The >>latest version 1.10.3 builds correctly on Bioconductor's Windows and OS >>X machines but fails on Ubuntu: >> >> >>https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_chec >>kResults_release_bioc-2DLATEST_variancePartition_malbec2-2Dbuildsrc.html& >>d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKa >>aPhzWA&m=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6cCw&s=RBYxTA_a5mlzemSuuk >>87tom-Q10dMclvh6KjhOGULDw&e= >> >> The code in the package has been stable, and I am not able to reproduce >>the error on by Ubuntu machine 14.04.5 LTS with R 3.5.1. >> >> The issue has something to do with multithreading using doParallel. >>The error is: >> >> Warning in socketConnection("localhost", port = port, server = TRUE, >>blocking = TRUE, : >> port 11104 cannot be opened >> Quitting from lines 102-154 (variancePartition.Rnw) >> Error: processing vignette 'variancePartition.Rnw' failed with >>diagnostics: >> cannot open the connection >> Execution halted >> >> With the Bioconductor 3.7 Freeze coming, I�m concerned about getting >>stuck with a broken package. >> >> Thanks, >> - Gabriel >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> >>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman >>_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd >>GbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6c >>Cw&s=5WZzTZGK1jX2QI5fKn_INmjLYyv876INVFqftwFxlT4&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
