Re: [Bioc-devel] Changes S4Vectors etc.

2017-02-09 Thread Leonard Goldstein 
Hi Martin and Hervé,

The problem lies in the pre-built binaries. Installing SGSeq from source
fixes the installation. I bumped the version number for SGSeq to trigger a
rebuild, but I guess other packages are affected as well. Among SGSeq
dependencies it looks like Rsamtools needs a version bump too.

Thanks,

Leonard


On Thu, Feb 9, 2017 at 4:19 AM, Martin Morgan  wrote:

> On 02/09/2017 06:25 AM, Hervé Pagès wrote:
>
>> Hi Leonard,
>>
>> mmh... I can't reproduce this and it doesn't show up on the build report
>> either. But I got another strange error when I tried to *install*
>> SGSeq: something about TxFeatures not being able to extend GenomicRanges
>> because of incompatible type for the elementMetadata slot.
>>
>> I got rid of it by re-installing GenomicRanges from svn.
>> I guess I had some stalled class definition somewhere in a cache.
>>
>> Looks like maybe you also have a stalled class definition somewhere
>> in a cache for one of SGFeatureCounts's parent classes. Not sure which
>> one though :-/
>>
>> Maybe I forgot to bump a package version somewhere after I renamed
>> characterORNULL -> character_OR_NULL? Re-installing S4Vectors, IRanges,
>> GenomicRanges, and SummarizedExperiment directly from svn might help.
>>
>
> See also https://support.bioconductor.org/p/92201/#92205 where
>
> GeneSetCollection extends 'list', which extends 'vector'
>
> GSEABase Depends: on annotate which Depends: on AnnotationDbi which
> Imports: S4Vectors.
>
> S4Vectors defines a class union on vector_OR_factor (previously
> vectorORfactor). Consequently, GeneSetCollection extends vector_OR_factor.
>
> Class definitions are cached at package installation time, so GSEABase
> class definitions became out-of-date when S4Vectors was updated.
>
> A conservative approach is to bump the version of all packages that depend
> on S4Vectors, even GSEABase which is three steps away from S4Vectors. I
> believe that this involves
>
>   db = available.packages(repos=BiocInstaller::biocinstallRepos()[1])
>   revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE,
>   reverse=TRUE)
>
> which is
>
> > length(revdeps$S4Vectors)
> [1] 662
>
> packages!
>
> Leonard could find candidates for re-installation with
>
> > mydep = tools::package_dependencies("SGSeq", db, recursive=TRUE)
> > mydep$SGSeq[mydep$SGSeq %in% revdeps$S4Vectors]
>  [1] "IRanges"  "GenomicRanges""Rsamtools"
>  [4] "SummarizedExperiment" "AnnotationDbi""Biostrings"
>  [7] "GenomicAlignments""GenomicFeatures"  "GenomeInfoDb"
> [10] "rtracklayer"  "XVector"  "biomaRt"
> [13] "DelayedArray"
>
> Martin
>
>
>
>> Cheers,
>> H.
>>
>> On 02/08/2017 04:18 PM, Leonard Goldstein wrote:
>>
>>> Hi Hervé,
>>>
>>> It looks like there have been some changes in bioc-devel (S4Vectors etc.)
>>> that break the SGSeq package (see below). I'm not sure whether this is
>>> something that needs to be addressed in SGSeq or its dependencies. I'd be
>>> grateful for any pointers. Thanks for your help.
>>>
>>> Leonard
>>>
>>> --
>>>
 example(makeSGFeatureCounts, "SGSeq")

>>>
>>> mkSGFC> sgfc <- makeSGFeatureCounts(sgf_pred, si,
>>> mkSGFC+   matrix(0L, length(sgf_pred), nrow(si)))
>>> Error in checkSlotAssignment(object, name, value) :
>>>   assignment of an object of class "NULL" is not valid for slot
>>> 'NAMES' in
>>> an object of class "SGFeatureCounts"; is(value, "characterORNULL") is not
>>> TRUE
>>>

 sessionInfo()

>>> R Under development (unstable) (2017-02-06 r72129)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: OS X El Capitan 10.11.6
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats4parallel  stats graphics  grDevices utils datasets
>>> [8] methods   base
>>>
>>> other attached packages:
>>>  [1] SGSeq_1.9.1SummarizedExperiment_1.5.5
>>>  [3] DelayedArray_0.1.4 Biobase_2.35.0
>>>  [5] Rsamtools_1.27.12  Biostrings_2.43.4
>>>  [7] XVector_0.15.2 GenomicRanges_1.27.22
>>>  [9] GenomeInfoDb_1.11.9IRanges_2.9.18
>>> [11] S4Vectors_0.13.13  BiocGenerics_0.21.3
>>>
>>> loaded via a namespace (and not attached):
>>>  [1] igraph_1.0.1 Rcpp_0.12.9
>>> AnnotationDbi_1.37.2
>>>
>>>  [4] magrittr_1.5 zlibbioc_1.21.0
>>>  GenomicAlignments_1.11.9
>>>  [7] BiocParallel_1.9.5   lattice_0.20-34  tools_3.4.0
>>>
>>> [10] grid_3.4.0   DBI_0.5-1digest_0.6.12
>>>
>>> [13] Matrix_1.2-8 GenomeInfoDbData_0.99.0  rtracklayer_1.35.5
>>>
>>> [16] bitops_1.0-6 RUnit_0.4.31 biomaRt_2.31.4
>>>
>>> [19] RCurl_1.95-4.8   memoise_1.0.0RSQLite_1.1-2
>>>
>>> [22] compiler_3.4.0   GenomicFeatures_1.27.6   XML_3.98-1.5
>>>
>>>

>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>>

Re: [Bioc-devel] Changes S4Vectors etc.

2017-02-09 Thread Hervé Pagès 

Hi Leonard,

mmh... I can't reproduce this and it doesn't show up on the build report
either. But I got another strange error when I tried to *install*
SGSeq: something about TxFeatures not being able to extend GenomicRanges
because of incompatible type for the elementMetadata slot.

I got rid of it by re-installing GenomicRanges from svn.
I guess I had some stalled class definition somewhere in a cache.

Looks like maybe you also have a stalled class definition somewhere
in a cache for one of SGFeatureCounts's parent classes. Not sure which
one though :-/

Maybe I forgot to bump a package version somewhere after I renamed
characterORNULL -> character_OR_NULL? Re-installing S4Vectors, IRanges,
GenomicRanges, and SummarizedExperiment directly from svn might help.

Cheers,
H.

On 02/08/2017 04:18 PM, Leonard Goldstein wrote:

Hi Hervé,

It looks like there have been some changes in bioc-devel (S4Vectors etc.)
that break the SGSeq package (see below). I'm not sure whether this is
something that needs to be addressed in SGSeq or its dependencies. I'd be
grateful for any pointers. Thanks for your help.

Leonard

--

example(makeSGFeatureCounts, "SGSeq")


mkSGFC> sgfc <- makeSGFeatureCounts(sgf_pred, si,
mkSGFC+   matrix(0L, length(sgf_pred), nrow(si)))
Error in checkSlotAssignment(object, name, value) :
  assignment of an object of class "NULL" is not valid for slot 'NAMES' in
an object of class "SGFeatureCounts"; is(value, "characterORNULL") is not
TRUE


sessionInfo()

R Under development (unstable) (2017-02-06 r72129)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:
[1] C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] SGSeq_1.9.1SummarizedExperiment_1.5.5
 [3] DelayedArray_0.1.4 Biobase_2.35.0
 [5] Rsamtools_1.27.12  Biostrings_2.43.4
 [7] XVector_0.15.2 GenomicRanges_1.27.22
 [9] GenomeInfoDb_1.11.9IRanges_2.9.18
[11] S4Vectors_0.13.13  BiocGenerics_0.21.3

loaded via a namespace (and not attached):
 [1] igraph_1.0.1 Rcpp_0.12.9  AnnotationDbi_1.37.2

 [4] magrittr_1.5 zlibbioc_1.21.0
 GenomicAlignments_1.11.9
 [7] BiocParallel_1.9.5   lattice_0.20-34  tools_3.4.0

[10] grid_3.4.0   DBI_0.5-1digest_0.6.12

[13] Matrix_1.2-8 GenomeInfoDbData_0.99.0  rtracklayer_1.35.5

[16] bitops_1.0-6 RUnit_0.4.31 biomaRt_2.31.4

[19] RCurl_1.95-4.8   memoise_1.0.0RSQLite_1.1-2

[22] compiler_3.4.0   GenomicFeatures_1.27.6   XML_3.98-1.5





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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

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[Bioc-devel] Changes S4Vectors etc.

2017-02-08 Thread Leonard Goldstein 
Hi Hervé,

It looks like there have been some changes in bioc-devel (S4Vectors etc.)
that break the SGSeq package (see below). I'm not sure whether this is
something that needs to be addressed in SGSeq or its dependencies. I'd be
grateful for any pointers. Thanks for your help.

Leonard

--
> example(makeSGFeatureCounts, "SGSeq")

mkSGFC> sgfc <- makeSGFeatureCounts(sgf_pred, si,
mkSGFC+   matrix(0L, length(sgf_pred), nrow(si)))
Error in checkSlotAssignment(object, name, value) :
  assignment of an object of class "NULL" is not valid for slot 'NAMES' in
an object of class "SGFeatureCounts"; is(value, "characterORNULL") is not
TRUE
>
> sessionInfo()
R Under development (unstable) (2017-02-06 r72129)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:
[1] C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] SGSeq_1.9.1SummarizedExperiment_1.5.5
 [3] DelayedArray_0.1.4 Biobase_2.35.0
 [5] Rsamtools_1.27.12  Biostrings_2.43.4
 [7] XVector_0.15.2 GenomicRanges_1.27.22
 [9] GenomeInfoDb_1.11.9IRanges_2.9.18
[11] S4Vectors_0.13.13  BiocGenerics_0.21.3

loaded via a namespace (and not attached):
 [1] igraph_1.0.1 Rcpp_0.12.9  AnnotationDbi_1.37.2

 [4] magrittr_1.5 zlibbioc_1.21.0
 GenomicAlignments_1.11.9
 [7] BiocParallel_1.9.5   lattice_0.20-34  tools_3.4.0

[10] grid_3.4.0   DBI_0.5-1digest_0.6.12

[13] Matrix_1.2-8 GenomeInfoDbData_0.99.0  rtracklayer_1.35.5

[16] bitops_1.0-6 RUnit_0.4.31 biomaRt_2.31.4

[19] RCurl_1.95-4.8   memoise_1.0.0RSQLite_1.1-2

[22] compiler_3.4.0   GenomicFeatures_1.27.6   XML_3.98-1.5

>

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