Re: [Bioc-devel] Bioconductor package build fails

[Martin Morgan]

It might make sense to seriously throttle your use of parallel evaluation in 
your vignette / example code, perhaps even defaulting to serial evaluation. 
This is also relevant to resource use on the build machines. I'm not really 
sure of the details but it seems like the problem is that the socket cluster is 
trying to use a particular port, maybe chosen randomly from a range, and it 
turns out that the port is already in use, e.g., by another package being built.

Martin

On 10/11/18, 7:11 PM, "Bioc-devel on behalf of Hoffman, Gabriel" 
 wrote:

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"  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=DwIFaQ=shNJtf5dKgNcPZ6Yh64b-A=KdYcmw5SdXylMrTGSuNVk
>NJulowod64k0PTDC5BHZkk=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E=3jM
>Ia0up64DNhDmFncfoVMDawXZIKv8OCyswMc8VWQ0=
>LAPACK: 
>/home/hpages/R/R-3.5.1/lib/https://urldefense.proofpoint.com/v2/url?u=http
>-3A__libRlapack.so=DwIFaQ=shNJtf5dKgNcPZ6Yh64b-A=KdYcmw5SdXylMrTGSuN
>VkNJulowod64k0PTDC5BHZkk=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E=M
>8hFMwj_eBOoEvdwmXC3h7J_VmhrPPNwg5B7giSrSSs=
>
>locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel  stats graphics  grDevices utils datasets
>[8] methods   base
>
>other attached packages:
>  [1] dendextend_1.8.0ballgown_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_0.18.3edgeR_3.22.5
>[13] lme4_1.1-18-1   Matrix_1.2-14
>[15] doParallel_1.0.14   iterators_1.0.10
>[17] variancePartition_1.10.3Biobase_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_0.2-22colorRamps_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_1.2-3nloptr_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_1.4.1htmltools_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] 

Re: [Bioc-devel] Bioconductor package build fails

[Hoffman, Gabriel]

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"  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=DwIFaQ=shNJtf5dKgNcPZ6Yh64b-A=KdYcmw5SdXylMrTGSuNVk
>NJulowod64k0PTDC5BHZkk=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E=3jM
>Ia0up64DNhDmFncfoVMDawXZIKv8OCyswMc8VWQ0=
>LAPACK: 
>/home/hpages/R/R-3.5.1/lib/https://urldefense.proofpoint.com/v2/url?u=http
>-3A__libRlapack.so=DwIFaQ=shNJtf5dKgNcPZ6Yh64b-A=KdYcmw5SdXylMrTGSuN
>VkNJulowod64k0PTDC5BHZkk=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E=M
>8hFMwj_eBOoEvdwmXC3h7J_VmhrPPNwg5B7giSrSSs=
>
>locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel  stats graphics  grDevices utils datasets
>[8] methods   base
>
>other attached packages:
>  [1] dendextend_1.8.0ballgown_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_0.18.3edgeR_3.22.5
>[13] lme4_1.1-18-1   Matrix_1.2-14
>[15] doParallel_1.0.14   iterators_1.0.10
>[17] variancePartition_1.10.3Biobase_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_0.2-22colorRamps_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_1.2-3nloptr_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_1.4.1htmltools_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_1.3.1gtools_3.8.1
>
>  [49] XML_3.98-1.16DEoptimR_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_1.1.0gridExtra_2.3
>
>  [58] rpart_4.1-13 latticeExtra_0.6-28  stringi_1.2.4
>
>  [61] RSQLite_2.1.1genefilter_1.62.0checkmate_1.8.5
>
>  [64] 
>caTools_https://urldefense.proofpoint.com/v2/url?u=http-3A__1.17.1.1=DwI
>FaQ=shNJtf5dKgNcPZ6Yh64b-A=KdYcmw5SdXylMrTGSuNVkNJulowod64k0PTDC5BHZkk
>=KuNqEpeopBuZGxLxcykyI2_IwkJE_oSorni83Ae717E=c5XRWImsmPTHqu8vDjbP_MZ-k
>E4pZylRmN0EZMQIqlA= 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  

Re: [Bioc-devel] Bioconductor package build fails

[Hervé Pagès]

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

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] dendextend_1.8.0ballgown_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_0.18.3edgeR_3.22.5
[13] lme4_1.1-18-1   Matrix_1.2-14
[15] doParallel_1.0.14   iterators_1.0.10
[17] variancePartition_1.10.3Biobase_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_0.2-22colorRamps_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_1.2-3nloptr_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_1.4.1htmltools_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_1.3.1gtools_3.8.1 

 [49] XML_3.98-1.16DEoptimR_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_1.1.0gridExtra_2.3 

 [58] rpart_4.1-13 latticeExtra_0.6-28  stringi_1.2.4 

 [61] RSQLite_2.1.1genefilter_1.62.0checkmate_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_1.0.0pillar_1.3.0 

 [85] whisker_0.3-2foreign_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_1.11.8blob_1.1.1   diptest_0.75-7 

[103] digest_0.6.18xtable_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 

Re: [Bioc-devel] Problem with setClassUnion and DelayedArray

[Elizabeth Purdom]

Thanks so much Hervé! That appears to have solved the problem. And I will 
definitely keep in mind for the future Michael’s suggestion of duck typing for 
matrix-like objects. 

All of the best,
Elizabeth

> On Oct 10, 2018, at 9:33 PM, Hervé Pagès  wrote:
> 
> Hi Elizabeth,
> 
> I agree that the setClassUnion() warning is rather esoteric, especially
> the "consider setClassUnion()" part.
> 
>  library(DelayedArray)
>  setClassUnion("matrixOrHDF5", c("matrix", "DelayedArray"))
>  # Warning message:
>  # subclass "DelayedArray1" of class "DelayedArray" is not local and
>  # cannot be updated for new inheritance information; consider
> 
> Furthermore, showClass("DelayedArray") reports the correct inheritance
> information:
> 
>  showClass("DelayedArray1")
>  # Class "DelayedArray1" [package "DelayedArray"]
>  #
>  # Slots:
>  #
>  # Name:index delayed_opsseed
>  # Class:listlist ANY
>  #
>  # Extends:
>  # Class "DelayedArray", directly
>  # Class "DelayedUnaryIsoOp", by class "DelayedArray", distance 2
>  # Class "matrixOrHDF5", by class "DelayedArray", distance 2
>  # Class "DelayedUnaryOp", by class "DelayedArray", distance 3
>  # Class "DelayedOp", by class "DelayedArray", distance 4
>  # Class "Array", by class "DelayedArray", distance 5
> 
> As well as extends():
> 
>  extends("DelayedArray1")
>  # [1] "DelayedArray1" "DelayedArray"  "DelayedUnaryIsoOp"
>  # [4] "matrixOrHDF5"  "DelayedUnaryOp""DelayedOp"
>  # [7] "Array"
> 
>  extends("DelayedArray", "matrixOrHDF5")
>  # [1] TRUE
> 
>  extends("DelayedArray1", "DelayedArray")
>  # [1] TRUE
> 
>  extends("DelayedArray1", "matrixOrHDF5")
>  # [1] TRUE
> 
> So it might just be a spurious warning :-/
> 
> Anyway, I've exported the DelayedArray1 class in DelayedArray 0.7.48:
> 
> https://github.com/Bioconductor/DelayedArray/commit/26061a9b28b87b8a3ee26b8b81ff3334b55115c1
> 
> No more warning with this version:
> 
>  library(DelayedArray)
>  setClassUnion("matrixOrHDF5", c("matrix", "DelayedArray"))
> 
> Cheers,
> H.
> 
> 
> On 10/10/2018 11:51 AM, Elizabeth Purdom wrote:
>> Hello,
>> I am using `setClassUnion` in my package `clusterExperiment` in the 
>> following code to allow for either matrix or DelayedArray:
>> setClassUnion("matrixOrHDF5",members=c("matrix", "DelayedArray"))
>> This causes the following warning in checking my package:
>> Warning: subclass "DelayedArray1" of class "DelayedArray" is not local and 
>> cannot be updated for new inheritance information; consider setClassUnion()
>> I’ve gotten this warning in other settings, and I believe it is due to the 
>> fact that setClassUnion works on the subclasses of the members, so if you 
>> give the argument `members=c(“X”,”Y”)` and you haven’t imported into your 
>> package all of the subclasses of “X” and “Y” it is warning you those 
>> non-imported classes haven’t been dealt with (though if so, I’d say the 
>> warning is awfully cryptic, especially since it says to use `setClassUnion` 
>> as a solution). In my other cases, I have just gone ahead and imported all 
>> of the subclasses from the package that defines the member classes and have 
>> gotten rid of the message (in the past it hasn’t been so many). But 
>> “DelayedArray1” is not an exported class of the DelayedArray package so that 
>> is not an option here.
>> I have been just ignoring this warning, since I understand (I think) the 
>> warning, I can’t do anything about it, and am not concerned about it since 
>> this new class is only used internally by my function for the slot 
>> definition. And I don’t think the user sees this generally. But given that 
>> we’re coming up on a release I thought I would ask if there’s anything I can 
>> do to get rid of this warning! Or can I go with my first instinct and safely 
>> ignore it?
>> Thanks,
>> Elizabeth Purdom
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=4le20lkIbxVE8gFC4uH_tCGjq9qX1garrTomLOEFN6A=VePKILIDYgQk9KdF7u7hJQJLglF5ga8I6M5u99inEyo=
> 
> -- 
> 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

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[Bioc-devel] Bioconductor package build fails

[Hoffman, Gabriel]

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:

http://bioconductor.org/checkResults/release/bioc-LATEST/variancePartition/malbec2-buildsrc.html

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]]

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Re: [Bioc-devel] Have trouble in push to master branch

[Zhu, Lihua (Julie)]

Nitesh,
Thanks for fixing the issue! It works now.
Best regards,
Julie

On 10/11/18, 1:55 PM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

Thank you Nitesh,



It works now.



Jianhong.



On 10/11/18, 1:53 PM, "Turaga, Nitesh"  
wrote:



Please try now. 



> On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie) 
 wrote:

> 

> Nitesh,

> 

> I encountered the same issue with CRISPRseek package. Could you 
please help? Thanks!

> 

> To 
https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org=DwIGaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=Rh4TcF-7dtBYsUoyoYakR6JT33jjesIPuWLpYOe0MTw=FQiC3JrYfggdNOkIvKFD1YBWJOwwr2ukBOgSW7K-Ihg=:packages/CRISPRseek.git

> ! [remote rejected] master -> master (pre-receive hook declined)

> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/CRISPRseek.git'

> 

> Best regards,

> 

> Julie

> 

> On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" 
 
wrote:

> 

>Hi Jianhong,

> 

> 

> 

>I’m looking into it now. 

> 

> 

> 

>Nitesh 

> 

> 

> 

>> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D. 
 wrote:

> 

>> 

> 

>> Hi,

> 

>> 

> 

>> I am trying to fix bug in my package. However, I got declined 
message:

> 

>> 

> 

>> 

> 

>> git push upstream master

> 

>> 

> 

>> Counting objects: 38, done.

> 

>> 

> 

>> Delta compression using up to 8 threads.

> 

>> 

> 

>> Compressing objects: 100% (26/26), done.

> 

>> 

> 

>> Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.

> 

>> 

> 

>> Total 38 (delta 30), reused 16 (delta 12)

> 

>> 

> 

>> remote: Traceback (most recent call last):

> 

>> 

> 

>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", 
line 104, in 

> 

>> 

> 

>> remote: hooks_dict = read_bioc_conf(conf)

> 

>> 

> 

>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", 
line 60, in read_bioc_conf

> 

>> 

> 

>> remote: for hook in d[package]:

> 

>> 

> 

>> remote: KeyError: 'Package: NADfinder'

> 

>> 

> 

>> To 
https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org=DwIGaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=ldl4cdibkRktwLiyZ6niwklGYISVFGeXm27fs_BVZbo=X0WooCCk3_DxndJDvyJOOlMSACg6AVEER4VTQcjlcEw=:packages/NADfinder.git

> 

>> 

> 

>> ! [remote rejected] master -> master (pre-receive hook declined)

> 

>> 

> 

>> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/NADfinder.git'

> 

>> 

> 

>> How could I fix this? Thank you for your help.

> 

>> 

> 

>> Yours Sincerely,

> 

>> 

> 

>> Jianhong Ou

> 

>> 

> 

>> Email: jianhong...@duke.edu

> 

>> Bioinformatician II

> 

>> Department of Cell Biology

> 

>> Duke University School of Medicine

> 

>> Durham, NC, 27710

> 

>> 

> 

>> Confidentiality Notice:

> 

>> This e-mail message, including any attachments, is for the sole use 
of the intended recipient(s) and may contain confidential, proprietary and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender immediately and destroy or permanently delete all copies of 
the original message.

> 

>> 

Re: [Bioc-devel] Have trouble in push to master branch

[Jianhong Ou, Ph.D.]

Thank you Nitesh,

It works now.

Jianhong.

On 10/11/18, 1:53 PM, "Turaga, Nitesh"  wrote:

Please try now. 

> On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie)  
wrote:
> 
> Nitesh,
> 
> I encountered the same issue with CRISPRseek package. Could you please 
help? Thanks!
> 
> To git.bioconductor.org:packages/CRISPRseek.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/CRISPRseek.git'
> 
> Best regards,
> 
> Julie
> 
> On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" 
 
wrote:
> 
>Hi Jianhong,
> 
> 
> 
>I’m looking into it now. 
> 
> 
> 
>Nitesh 
> 
> 
> 
>> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D.  
wrote:
> 
>> 
> 
>> Hi,
> 
>> 
> 
>> I am trying to fix bug in my package. However, I got declined message:
> 
>> 
> 
>> 
> 
>> git push upstream master
> 
>> 
> 
>> Counting objects: 38, done.
> 
>> 
> 
>> Delta compression using up to 8 threads.
> 
>> 
> 
>> Compressing objects: 100% (26/26), done.
> 
>> 
> 
>> Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.
> 
>> 
> 
>> Total 38 (delta 30), reused 16 (delta 12)
> 
>> 
> 
>> remote: Traceback (most recent call last):
> 
>> 
> 
>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 
104, in 
> 
>> 
> 
>> remote: hooks_dict = read_bioc_conf(conf)
> 
>> 
> 
>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 
60, in read_bioc_conf
> 
>> 
> 
>> remote: for hook in d[package]:
> 
>> 
> 
>> remote: KeyError: 'Package: NADfinder'
> 
>> 
> 
>> To 
https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org=DwIGaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=ldl4cdibkRktwLiyZ6niwklGYISVFGeXm27fs_BVZbo=X0WooCCk3_DxndJDvyJOOlMSACg6AVEER4VTQcjlcEw=:packages/NADfinder.git
> 
>> 
> 
>> ! [remote rejected] master -> master (pre-receive hook declined)
> 
>> 
> 
>> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/NADfinder.git'
> 
>> 
> 
>> How could I fix this? Thank you for your help.
> 
>> 
> 
>> Yours Sincerely,
> 
>> 
> 
>> Jianhong Ou
> 
>> 
> 
>> Email: jianhong...@duke.edu
> 
>> Bioinformatician II
> 
>> Department of Cell Biology
> 
>> Duke University School of Medicine
> 
>> Durham, NC, 27710
> 
>> 
> 
>> Confidentiality Notice:
> 
>> This e-mail message, including any attachments, is for the sole use of 
the intended recipient(s) and may contain confidential, proprietary and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender immediately and destroy or permanently delete all copies of 
the original message.
> 
>> 
> 
>>  [[alternative HTML version deleted]]
> 
>> 
> 
>> ___
> 
>> Bioc-devel@r-project.org mailing list
> 
>> 
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> 
> 
> 
> 
> 
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Re: [Bioc-devel] Have trouble in push to master branch

[Turaga, Nitesh]

Please try now. 

> On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie)  
> wrote:
> 
> Nitesh,
> 
> I encountered the same issue with CRISPRseek package. Could you please help? 
> Thanks!
> 
> To git.bioconductor.org:packages/CRISPRseek.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/CRISPRseek.git'
> 
> Best regards,
> 
> Julie
> 
> On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" 
>  
> wrote:
> 
>Hi Jianhong,
> 
> 
> 
>I’m looking into it now. 
> 
> 
> 
>Nitesh 
> 
> 
> 
>> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D.  wrote:
> 
>> 
> 
>> Hi,
> 
>> 
> 
>> I am trying to fix bug in my package. However, I got declined message:
> 
>> 
> 
>> 
> 
>> git push upstream master
> 
>> 
> 
>> Counting objects: 38, done.
> 
>> 
> 
>> Delta compression using up to 8 threads.
> 
>> 
> 
>> Compressing objects: 100% (26/26), done.
> 
>> 
> 
>> Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.
> 
>> 
> 
>> Total 38 (delta 30), reused 16 (delta 12)
> 
>> 
> 
>> remote: Traceback (most recent call last):
> 
>> 
> 
>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 104, 
>> in 
> 
>> 
> 
>> remote: hooks_dict = read_bioc_conf(conf)
> 
>> 
> 
>> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 60, 
>> in read_bioc_conf
> 
>> 
> 
>> remote: for hook in d[package]:
> 
>> 
> 
>> remote: KeyError: 'Package: NADfinder'
> 
>> 
> 
>> To 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org=DwIGaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=ldl4cdibkRktwLiyZ6niwklGYISVFGeXm27fs_BVZbo=X0WooCCk3_DxndJDvyJOOlMSACg6AVEER4VTQcjlcEw=:packages/NADfinder.git
> 
>> 
> 
>> ! [remote rejected] master -> master (pre-receive hook declined)
> 
>> 
> 
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/NADfinder.git'
> 
>> 
> 
>> How could I fix this? Thank you for your help.
> 
>> 
> 
>> Yours Sincerely,
> 
>> 
> 
>> Jianhong Ou
> 
>> 
> 
>> Email: jianhong...@duke.edu
> 
>> Bioinformatician II
> 
>> Department of Cell Biology
> 
>> Duke University School of Medicine
> 
>> Durham, NC, 27710
> 
>> 
> 
>> Confidentiality Notice:
> 
>> This e-mail message, including any attachments, is for the sole use of the 
>> intended recipient(s) and may contain confidential, proprietary and 
>> privileged information. Any unauthorized review, use, disclosure or 
>> distribution is prohibited. If you are not the intended recipient, please 
>> contact the sender immediately and destroy or permanently delete all copies 
>> of the original message.
> 
>> 
> 
>>  [[alternative HTML version deleted]]
> 
>> 
> 
>> ___
> 
>> Bioc-devel@r-project.org mailing list
> 
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> 
> 
> 
> 
> 
>This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] Have trouble in push to master branch

[Zhu, Lihua (Julie)]

Nitesh,

I encountered the same issue with CRISPRseek package. Could you please help? 
Thanks!

To git.bioconductor.org:packages/CRISPRseek.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/CRISPRseek.git'

Best regards,

Julie

On 10/11/18, 1:43 PM, "Bioc-devel on behalf of Turaga, Nitesh" 
 
wrote:

Hi Jianhong,



I’m looking into it now. 



Nitesh 



> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D.  
wrote:

> 

> Hi,

> 

> I am trying to fix bug in my package. However, I got declined message:

> 

> 

> git push upstream master

> 

> Counting objects: 38, done.

> 

> Delta compression using up to 8 threads.

> 

> Compressing objects: 100% (26/26), done.

> 

> Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.

> 

> Total 38 (delta 30), reused 16 (delta 12)

> 

> remote: Traceback (most recent call last):

> 

> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 
104, in 

> 

> remote: hooks_dict = read_bioc_conf(conf)

> 

> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 
60, in read_bioc_conf

> 

> remote: for hook in d[package]:

> 

> remote: KeyError: 'Package: NADfinder'

> 

> To 
https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org=DwIGaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=ldl4cdibkRktwLiyZ6niwklGYISVFGeXm27fs_BVZbo=X0WooCCk3_DxndJDvyJOOlMSACg6AVEER4VTQcjlcEw=:packages/NADfinder.git

> 

> ! [remote rejected] master -> master (pre-receive hook declined)

> 

> error: failed to push some refs to 
'g...@git.bioconductor.org:packages/NADfinder.git'

> 

> How could I fix this? Thank you for your help.

> 

> Yours Sincerely,

> 

> Jianhong Ou

> 

> Email: jianhong...@duke.edu

> Bioinformatician II

> Department of Cell Biology

> Duke University School of Medicine

> Durham, NC, 27710

> 

> Confidentiality Notice:

> This e-mail message, including any attachments, is for the sole use of 
the intended recipient(s) and may contain confidential, proprietary and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender immediately and destroy or permanently delete all copies of 
the original message.

> 

>   [[alternative HTML version deleted]]

> 

> ___

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Re: [Bioc-devel] Have trouble in push to master branch

[Turaga, Nitesh]

Hi Jianhong,

I’m looking into it now. 

Nitesh 

> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D.  wrote:
> 
> Hi,
> 
> I am trying to fix bug in my package. However, I got declined message:
> 
> 
> git push upstream master
> 
> Counting objects: 38, done.
> 
> Delta compression using up to 8 threads.
> 
> Compressing objects: 100% (26/26), done.
> 
> Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.
> 
> Total 38 (delta 30), reused 16 (delta 12)
> 
> remote: Traceback (most recent call last):
> 
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 104, 
> in 
> 
> remote: hooks_dict = read_bioc_conf(conf)
> 
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 60, in 
> read_bioc_conf
> 
> remote: for hook in d[package]:
> 
> remote: KeyError: 'Package: NADfinder'
> 
> To git.bioconductor.org:packages/NADfinder.git
> 
> ! [remote rejected] master -> master (pre-receive hook declined)
> 
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/NADfinder.git'
> 
> How could I fix this? Thank you for your help.
> 
> Yours Sincerely,
> 
> Jianhong Ou
> 
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
> 
> Confidentiality Notice:
> This e-mail message, including any attachments, is for the sole use of the 
> intended recipient(s) and may contain confidential, proprietary and 
> privileged information. Any unauthorized review, use, disclosure or 
> distribution is prohibited. If you are not the intended recipient, please 
> contact the sender immediately and destroy or permanently delete all copies 
> of the original message.
> 
>   [[alternative HTML version deleted]]
> 
> ___
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[Bioc-devel] Have trouble in push to master branch

[Jianhong Ou, Ph.D.]

Hi,

I am trying to fix bug in my package. However, I got declined message:


git push upstream master

Counting objects: 38, done.

Delta compression using up to 8 threads.

Compressing objects: 100% (26/26), done.

Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.

Total 38 (delta 30), reused 16 (delta 12)

remote: Traceback (most recent call last):

remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 104, in 


remote: hooks_dict = read_bioc_conf(conf)

remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 60, in 
read_bioc_conf

remote: for hook in d[package]:

remote: KeyError: 'Package: NADfinder'

To git.bioconductor.org:packages/NADfinder.git

 ! [remote rejected] master -> master (pre-receive hook declined)

error: failed to push some refs to 
'g...@git.bioconductor.org:packages/NADfinder.git'

How could I fix this? Thank you for your help.

Yours Sincerely,

Jianhong Ou

Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710

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[Bioc-devel] New Feature: Ability to control pre-receive hooks in a modular way is active

[Turaga, Nitesh]

Hello Core team and Maintainers, 

We have just launched a new feature to regulate packages on 
git.bioconductor.org. The feature gives the core team, the ability to easily 
“disable" hooks for each package (software, data-experiment, and workflow) as 
needed. 

The hooks should be modified using a config file called “hooks.conf” which is 
available inside the “hook_maintainer.git” repository inside 
git.bioconductor.org/admin. With the file, “hooks.conf" you can individually 
modify which hooks are disabled for each package. 

The “hooks.conf" assumes that THREE pre-receive hooks are applied to each 
software package 

1. pre-receive-hook-large-files : prevents large files > 5MB
2. pre-receive-hook-duplicate-commits: prevents duplicate commits
3. pre-receive-hook-version-numbers: prevents bad version numbers. 

The "hooks.conf" assumes that TWO pre-receive hooks are applied to each 
data-experiment and workflow package 

1. pre-receive-hook-duplicate-commits: prevents duplicate commits
2. pre-receive-hook-version-numbers: prevents bad version numbers. 

With “hooks.conf", you can disable a single or multiple hooks per package as 
needed by adding,

Package: 
pre-receive-hook-large-files: False
pre-receive-hook-duplicate-commits: False
pre-receive-hook-version-numbers: False

Core team members sometimes disable the hooks only for one commit to give 
special permission for a package, then it is important to note that the line in 
“hooks.conf" which disables the hook for the package, has to be removed. 


For maintainers,

If your package needs permission to disable a hook, clearly explain why the 
hook needs to be disabled. This is an extreme step, and you package should 
almost always fall under the regulations of these hooks. It is always better to 
discuss the issue on bioc-devel before trying to disable a hook.

If you have any questions about this new feature, please let me know.

Best,


Nitesh Turaga
Bioconductor Core Team





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Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

[Hervé Pagès]

Sounds good.

I should also mention that Rsamtools has pileup() that is available
on all platforms. Don't know how easy it would be to use to achieve
the kind of variant calling you're doing in MTseeker though...

Cheers,
H.

On 10/11/2018 04:35 AM, Tim Triche, Jr. wrote:

This makes sense. Windows users won’t be easily able to call variants across 
thousands of samples but at least the plotting, impact prediction, etc will 
work fine for them.

I will need to define things such that the variant calling is optional, which 
is not too absurd — I’ll add loading of MVRanges/MVRangesList objects from VCFs 
and move gmapR to suggests.

Personally I use the variant calling functionality regularly, but I have my 
doubts as to whether someone on Windows would even have enough RAM to call 
variants across 2000+ samples in a shot, so this is a good compromise.  
Everything else is, I believe, platform agnostic. This should work.

--t


On Oct 11, 2018, at 1:41 AM, Hervé Pagès  wrote:

And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
something meaningful with MTseeker.

Otherwise the trick below will make MTseeker available on Windows
but Windows users won't be able to accomplish anything meaningful
with it. In that case, marking the package as unsupported on Windows
would be preferable.

Hope this makes sense,

H.


On 10/10/2018 10:26 PM, Hervé Pagès wrote:
Hi Tim,
No platform-specific dontrun capabilities AFAIK but you can use
something like:
   if (requireNamespace("gmapR", quietly=TRUE)) {
   ...
   ...
   }
in your man pages.
You would also need to move gmapR from Imports to Suggests.
Then make sure that MTseeker passes 'R CMD check' **without**
the gmapR package being installed. You'll need to define and set
environment variable _R_CHECK_FORCE_SUGGESTS_ to 0 for this.
Do it with:
   export _R_CHECK_FORCE_SUGGESTS_=0
on Linux or Mac, or with:
   set _R_CHECK_FORCE_SUGGESTS_=0
on Windows.
Once MTseeker is accepted, we'll add a .BBSoptions file with special
directive:
   CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&
This will have the effect to set the environment variable on the
Windows build machines before running 'R CMD check' there.
So MTseeker will be supported and available on all platforms.
For MTseekerData: the package doesn't seem to make any use of gmapR
so you can probably remove gmapR from its Suggests field.
Hope this helps,
H.

On 10/10/2018 07:46 AM, Tim Triche, Jr. wrote:
it looks like gmapR does not support Windows, and as a result, my MTseeker
package cannot build on tokay1, so the Data package which requires it also
cannot build on tokay1.  Are there platform-specific dontrun capabilities?

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_MTseekerData-5Fbuildreport-5F20181010103212.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18=QNKSsmQnfEAQOTI0r8dDuW_d01XzL_cL1cb5QIElLxw=

Short of somehow forcing gmapR to build on Windows, which I believe is
beyond my control, is there a way to declare that parts of the MTseeker
package are unsupported/unsupportable on Windows?

I suppose I could cleave off the variant-recalling portions but that seems
a little ridiculous. The original goal was to take the non-NuMT reads from
a given alignment, realign (only) those to rCRS/RSRS, and call against
that, for better mitochondrial haplogroup inference. We're still working
towards the full version, but even just calling variants against rCRS with
indels is hugely useful, and the ability to screen out haplogroup-specific
variants while retaining indels, SNVs, etc. turns out to be VERY handy.
More generally, there isn't any equivalent (AFAIK) in BioC, at all.

--t

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--
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


--
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

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Re: [Bioc-devel] Package simulatorZ timeout under Windows on the release but not the devel branch

[Obenchain, Valerie]

Looks like this has cleared up in the Oct 10 report:

  https://www.bioconductor.org/checkResults/release/bioc-LATEST/

We send notifications about failures in release twice a week (Monday and 
Thursday). This could have been a transient problem but happened to occur on a 
day we send notifications. Unless this becomes consistent you can ignore it.

Thanks.
Valerie

On 10/9/18 3:00 PM, Yuqing Zhang wrote:

Hi all,

I received an email saying that my package, simulatorZ, is timing out. In
the current report, it is timing out under Windows in the release branch.
But it passes all builds and checks in the devel branch on all platforms
(on Windows it passes the check in about 5 minutes). I haven't changed
anything in the package, so I'm confused how I got this timeout issue...

Could anyone please advise what I need to do about this?

Thanks,
Yuqing






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Re: [Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

[Tim Triche, Jr.]

This makes sense. Windows users won’t be easily able to call variants across 
thousands of samples but at least the plotting, impact prediction, etc will 
work fine for them. 

I will need to define things such that the variant calling is optional, which 
is not too absurd — I’ll add loading of MVRanges/MVRangesList objects from VCFs 
and move gmapR to suggests. 

Personally I use the variant calling functionality regularly, but I have my 
doubts as to whether someone on Windows would even have enough RAM to call 
variants across 2000+ samples in a shot, so this is a good compromise.  
Everything else is, I believe, platform agnostic. This should work. 

--t

> On Oct 11, 2018, at 1:41 AM, Hervé Pagès  wrote:
> 
> And of course: the whole trick I described below only makes sense
> if MTseeker doesn't rely on gmapR for its core functionality, that
> is, if not having gmapR installed still allows the user to accomplish
> something meaningful with MTseeker.
> 
> Otherwise the trick below will make MTseeker available on Windows
> but Windows users won't be able to accomplish anything meaningful
> with it. In that case, marking the package as unsupported on Windows
> would be preferable.
> 
> Hope this makes sense,
> 
> H.
> 
>> On 10/10/2018 10:26 PM, Hervé Pagès wrote:
>> Hi Tim,
>> No platform-specific dontrun capabilities AFAIK but you can use
>> something like:
>>   if (requireNamespace("gmapR", quietly=TRUE)) {
>>   ...
>>   ...
>>   }
>> in your man pages.
>> You would also need to move gmapR from Imports to Suggests.
>> Then make sure that MTseeker passes 'R CMD check' **without**
>> the gmapR package being installed. You'll need to define and set
>> environment variable _R_CHECK_FORCE_SUGGESTS_ to 0 for this.
>> Do it with:
>>   export _R_CHECK_FORCE_SUGGESTS_=0
>> on Linux or Mac, or with:
>>   set _R_CHECK_FORCE_SUGGESTS_=0
>> on Windows.
>> Once MTseeker is accepted, we'll add a .BBSoptions file with special
>> directive:
>>   CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&
>> This will have the effect to set the environment variable on the
>> Windows build machines before running 'R CMD check' there.
>> So MTseeker will be supported and available on all platforms.
>> For MTseekerData: the package doesn't seem to make any use of gmapR
>> so you can probably remove gmapR from its Suggests field.
>> Hope this helps,
>> H.
>>> On 10/10/2018 07:46 AM, Tim Triche, Jr. wrote:
>>> it looks like gmapR does not support Windows, and as a result, my MTseeker
>>> package cannot build on tokay1, so the Data package which requires it also
>>> cannot build on tokay1.  Are there platform-specific dontrun capabilities?
>>> 
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_MTseekerData-5Fbuildreport-5F20181010103212.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18=QNKSsmQnfEAQOTI0r8dDuW_d01XzL_cL1cb5QIElLxw=
>>>  
>>> 
>>> Short of somehow forcing gmapR to build on Windows, which I believe is
>>> beyond my control, is there a way to declare that parts of the MTseeker
>>> package are unsupported/unsupportable on Windows?
>>> 
>>> I suppose I could cleave off the variant-recalling portions but that seems
>>> a little ridiculous. The original goal was to take the non-NuMT reads from
>>> a given alignment, realign (only) those to rCRS/RSRS, and call against
>>> that, for better mitochondrial haplogroup inference. We're still working
>>> towards the full version, but even just calling variants against rCRS with
>>> indels is hugely useful, and the ability to screen out haplogroup-specific
>>> variants while retaining indels, SNVs, etc. turns out to be VERY handy.
>>> More generally, there isn't any equivalent (AFAIK) in BioC, at all.
>>> 
>>> --t
>>> 
>>> [[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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18=rzPUqLBge6xE1TymeYxIxJxkiiOHefbSgzPOLYEhvrM=
>>>  
>>> 
> 
> -- 
> 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

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Re: [Bioc-devel] Why bioconductor?

[Lluís Revilla]

Some people is lost even when and how many updates are and differences
between different packages. See this question for instance (
https://www.biostars.org/p/287871/)
Compared to CRAN or PyPi, which don't have release cycles, Bioconductor
workflow is a bit more complicated to learn.

Related to Bioconductor style there is a issue on lintr to build one for
bioconductor: https://github.com/jimhester/lintr/issues/43
I think that with a few more tweaks to this file (
https://github.com/llrs/customizations/blob/master/.lintr) it could be
ready for the community. Pull requests are welcome.

There is also the styler package (https://github.com/r-lib/styler) which
automatically changes of style according to some rules.
I opened an issue about having Bioconductor style:
https://github.com/r-lib/styler/issues/331 but I couldn't manage to build
one style. It could be interesting to have one too.

Hope this helps





On Wed, 10 Oct 2018 at 23:43, Morgan, Martin 
wrote:

> I think pull requests on
>
>
>
> https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md
>
> would be welcome.
>
> Martin
>
> On 10/10/18 11:51 AM, Ludwig Geistlinger wrote:
> > While this might be obvious to most of us, it seems to be less clear to
> others.
> >
> > In particular, those who worked out their first package and wonder
> what's the difference between having a package available on Github, CRAN,
> or Bioconductor.
> >
> >
> > I wonder whether it would be helpful for the Bioc webpage to pick up on
> the benefits of submitting to CRAN by Hadley
> >
> >
> > http://r-pkgs.had.co.nz/release.html
> >
> >
> > and several considerations with respect to Bioconductor
> >
> >
> > https://bioinformatics.stackexchange.com/questions/639/why-bioconductor
> >
> >
> > (Maybe FAQ?)
> >
> >
> >   Just a thought.
> >
> >
> >   [[alternative HTML version deleted]]
> >
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> >
>
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