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.
Best,
H.
> 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
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] 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@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: 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
