[Bioc-devel] Bioconductor package build fails

Hervé Pagès hp@ge@ @ending from fredhutch@org
Fri Oct 12 01:01:53 CEST 2018

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.


 > 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/libRblas.so
LAPACK: /home/hpages/R/R-3.5.1/lib/libRlapack.so

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=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 
  [16] codetools_0.2-15         splines_3.5.1 
  [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 
  [43] gdata_2.18.0             nlme_3.1-137 
  [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 
  [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_1.17.1.1         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_checkResults_release_bioc-2DLATEST_variancePartition_malbec2-2Dbuildsrc.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6cCw&s=RBYxTA_a5mlzemSuuk87tom-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
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zy-TmtsjB4a5Mwg313kvmlN0-6yO-6JDYZsT1nV6cCw&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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