[Bioc-devel] Cannot reproduce build error

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Jan 7 11:49:12 CET 2020

Hi Jose,

evaluomeR 1.3.4 (master branch) is in BioC 3.11 (current BioC devel) so 
make sure that you use R 4.0 (current R devel) to develop/test the 
master branch of your package. This is what the build system uses to 
build/check all the packages in BioC 3.11. Also make sure that all your 
installed packages are up-to-date (run BiocManager::install() followed 
by BiocManager::valid() for that).

Using R 4.0 and up-to-date packages, I can reproduce the vignette error 
you see on the build report for BioC 3.11:

   > source("manual.R", echo=TRUE)
   > kOptTable <- getOptimalKValue(stabilityData, qualityData)
   Error in checkStabilityQualityData(stabData, qualData) :
     Stability data and quality data have different metrics

See my sessionInfo() and BiocManager::valid() below.

Note that the R-hub package builder uses R 3.6.1 to build evaluomeR 
1.3.4 so its results are meaningless/irrelevant.


 > sessionInfo()
R Under development (unstable) (2019-10-30 r77336)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:   /home/hpages/R/R-4.0.r77336/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.0.r77336/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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] evaluomeR_1.3.1             cluster_2.1.0
  [3] MultiAssayExperiment_1.13.4 SummarizedExperiment_1.17.1
  [5] DelayedArray_0.13.1         BiocParallel_1.21.2
  [7] matrixStats_0.55.0          Biobase_2.47.2
  [9] GenomicRanges_1.39.1        GenomeInfoDb_1.23.1
[11] IRanges_2.21.2              S4Vectors_0.25.8
[13] BiocGenerics_0.33.0         magrittr_1.5
[15] kableExtra_1.1.0            BiocStyle_2.15.3

loaded via a namespace (and not attached):
  [1] Rcpp_1.0.3             lattice_0.20-38        assertthat_0.2.1
  [4] zeallot_0.1.0          digest_0.6.23          plyr_1.8.5
  [7] R6_2.4.1               backports_1.1.5        evaluate_0.14
[10] httr_1.4.1             ggplot2_3.2.1          pillar_1.4.3
[13] Rdpack_0.11-1          zlibbioc_1.33.0        rlang_0.4.2
[16] lazyeval_0.2.2         rstudioapi_0.10        Matrix_1.2-18
[19] rmarkdown_2.0          webshot_0.5.2          readr_1.3.1
[22] stringr_1.4.0          RCurl_1.95-4.12        munsell_0.5.0
[25] compiler_4.0.0         xfun_0.11              pkgconfig_2.0.3
[28] htmltools_0.4.0        tidyselect_0.2.5       tibble_2.1.3
[31] GenomeInfoDbData_1.2.2 viridisLite_0.3.0      dplyr_0.8.3
[34] crayon_1.3.4           MASS_7.3-51.5          bitops_1.0-6
[37] grid_4.0.0             gtable_0.3.0           lifecycle_0.1.0
[40] scales_1.1.0           bibtex_0.4.2.2         stringi_1.4.3
[43] reshape2_1.4.3         XVector_0.27.0         xml2_1.2.2
[46] ggdendro_0.1-20        vctrs_0.2.1            tools_4.0.0
[49] glue_1.3.1             purrr_0.3.3            hms_0.5.2
[52] yaml_2.2.0             colorspace_1.4-1       BiocManager_1.30.10
[55] gbRd_0.4-11            rvest_0.3.5            corrplot_0.84
[58] knitr_1.26

 > BiocManager::valid()
[1] TRUE

On 1/7/20 01:22, José Antonio wrote:
> Hello everyone,
> I am having some troubles to reproduce the building error of our package:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_evaluomeR_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kyyYLcKIjU6AdBISzMul-STvNYSTpsBFPw-CyfWyoBM&s=Q5sEtTJ19qyBOoa6FWEOCleReg93yb_StBebWZUCw3c&e= 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_evaluomeR_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kyyYLcKIjU6AdBISzMul-STvNYSTpsBFPw-CyfWyoBM&s=Q5sEtTJ19qyBOoa6FWEOCleReg93yb_StBebWZUCw3c&e= 
>  >
> The error is related to the vignette generation, since inside of it 
> there is package code which seems to fail. I have tried to "R CMD build" 
> on Windows and Linux cloning the Bioconductor devel master branch but 
> the package builds fine from my side.
> Additionally, I have used "rhub" library to test this error in a machine 
> outside my environment and the "R CMD check" report builds fine (from 
> line 4033 onwards): 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__builder.r-2Dhub.io_status_evaluomeR-5F1.3.4.tar.gz-2Dff6d93551afc4ab198ee571ef43650c2-23L4033&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kyyYLcKIjU6AdBISzMul-STvNYSTpsBFPw-CyfWyoBM&s=WVy2bjdzwX8ips-19TqFLZ3IiF96P_b8Uu3v-JYVPZI&e= 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__builder.r-2Dhub.io_status_evaluomeR-5F1.3.4.tar.gz-2Dff6d93551afc4ab198ee571ef43650c2-23L4033&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kyyYLcKIjU6AdBISzMul-STvNYSTpsBFPw-CyfWyoBM&s=WVy2bjdzwX8ips-19TqFLZ3IiF96P_b8Uu3v-JYVPZI&e= 
>  >
> Could it be possible that somehow it is using old committed code causing 
> the vignette to crash?
> Thanks in advance,
> José Antonio
> _______________________________________________
> 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=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=kyyYLcKIjU6AdBISzMul-STvNYSTpsBFPw-CyfWyoBM&s=67JTVxl9mygKpex17pX0SL4szlX0jqq0stGpHp4Jb6g&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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