[Bioc-devel] Bioconductor package build fails
Hoffman, Gabriel
g@briel@hoffm@n @ending from m@@m@edu
Fri Oct 12 01:11:26 CEST 2018
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" <hpages using 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 using r-project.org mailing list
>>
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>>_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd
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>>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: hpages using fredhutch.org
>Phone: (206) 667-5791
>Fax: (206) 667-1319
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