Re: [Bioc-devel] EXTERNAL: Re: unknown build error novel bioc. package

[Maarten van Iterson]

Hi Marcel,

Thanks for looking into this. I fixed it and pushed. Lets see if the
package is building without errors now!

Cheers,
Maarten

On Wed, Dec 13, 2017 at 9:53 PM, Marcel Ramos <marcel.ra...@roswellpark.org>
wrote:

> Hi Maarten,
>
> Sorry about the confusion. The link you provided pointed to errors in
> *omicRexposome*.
>
> It appears that the errors you're getting for *omicsPrint* have to do
> with the `getGEO` call on
>
> line #261 in the vignette.
>
> It can be fixed if you introduce a `fileext` argument to `tempfile()`.
>
> Please see pull request # 3.
>
> Regards,
>
> Marcel
>
>
>
> On 12/13/2017 03:25 PM, Maarten van Iterson wrote:
>
> Hi Marcel,
>
> Thanks for your help, do you mean I should add "bgredata" to our DESCR
> file? omicsPrint should not depend on it?
>
> This sessionInfo when omicsPrint is loaded:
>
> > library(omicsPrint)
> Loading required package: MASS
> in method for ‘coerce’ with signature 
> ‘"RangedRaggedAssay","RaggedExperiment"’:
> no definition for class “RaggedExperiment”
> > sessionInfo()
> R Under development (unstable) (2017-09-30 r73418)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.3 LTS
>
> Matrix products: default
> BLAS: /usr/local/lib64/R/lib/libRblas.so
> LAPACK: /usr/local/lib64/R/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=nl_NL.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=nl_NL.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=nl_NL.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> other attached packages:
> [1] omicsPrint_0.99.30 MASS_7.3-47
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.14   compiler_3.5.0
>  [3] GenomeInfoDb_1.12.3plyr_1.8.4
>  [5] XVector_0.16.0 bitops_1.0-6
>  [7] tools_3.5.0zlibbioc_1.22.0
>  [9] digest_0.6.12  tibble_1.3.4
> [11] gtable_0.2.0   lattice_0.20-35
> [13] rlang_0.1.4Matrix_1.2-12
> [15] DelayedArray_0.2.7 shiny_1.0.5
> [17] parallel_3.5.0 gridExtra_2.3
> [19] GenomeInfoDbData_0.99.0stringr_1.2.0
> [21] UpSetR_1.3.3   S4Vectors_0.14.7
> [23] IRanges_2.10.5 stats4_3.5.0
> [25] MultiAssayExperiment_1.2.1 grid_3.5.0
> [27] shinydashboard_0.6.1   glue_1.2.0
> [29] Biobase_2.36.2 R6_2.2.2
> [31] purrr_0.2.4tidyr_0.7.2
> [33] magrittr_1.5   reshape2_1.4.2
> [35] ggplot2_2.2.1  scales_0.5.0
> [37] matrixStats_0.52.2 htmltools_0.3.6
> [39] BiocGenerics_0.22.1GenomicRanges_1.28.6
> [41] RaggedExperiment_1.0.0 SummarizedExperiment_1.6.5
> [43] mime_0.5   xtable_1.8-2
> [45] colorspace_1.3-2   httpuv_1.3.5
> [47] stringi_1.1.6  RCurl_1.95-4.8
> [49] lazyeval_0.2.1 munsell_0.4.3
>
>
>
>
> On Wed, Dec 13, 2017 at 8:52 PM, Marcel Ramos <
> marcel.ra...@roswellpark.org> wrote:
>
>> Hi Maarten,
>>
>> It appears that your vignette is pointing to a package that doesn't exist
>> in the build system.
>>
>> Please reference `package = "brgedata"` instead.
>>
>> Regards,
>> Marcel
>>
>>
>> *Note. Apologies if you've received this email twice.
>>
>> On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
>>
>> Dear all,
>>
>> Our new package, omicsPrint, has been accepted and added to the
>> bioconductor build system but is not passing through on any system. Locally
>> we are able to build install and execute the vignette. We have tried
>> several things without success.
>>
>> The current error we got for version 0.99.29 on malbec2 is:
>>
>> Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics:
>> parsing failed--expected only one '!series_data_table_begin'
>>
>> (https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
>>
>> )
>>
>> Anyone idea's or suggestions for debugging?
>>
>> Regards,
>> Maarten and Davy
>>
>>  [[alternative HTML version deleted]]
>>
>> ___bioc-de...@r-project.org 
>> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>> This email message may contain legally privileged and/or confidential
>>

Re: [Bioc-devel] unknown build error novel bioc. package

[Maarten van Iterson]

Hi Marcel,

Thanks for your help, do you mean I should add "bgredata" to our DESCR
file? omicsPrint should not depend on it?

This sessionInfo when omicsPrint is loaded:

> library(omicsPrint)
Loading required package: MASS
in method for ‘coerce’ with signature
‘"RangedRaggedAssay","RaggedExperiment"’: no definition for class
“RaggedExperiment”
> sessionInfo()
R Under development (unstable) (2017-09-30 r73418)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=nl_NL.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=nl_NL.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=nl_NL.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] omicsPrint_0.99.30 MASS_7.3-47

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14   compiler_3.5.0
 [3] GenomeInfoDb_1.12.3plyr_1.8.4
 [5] XVector_0.16.0 bitops_1.0-6
 [7] tools_3.5.0zlibbioc_1.22.0
 [9] digest_0.6.12  tibble_1.3.4
[11] gtable_0.2.0   lattice_0.20-35
[13] rlang_0.1.4Matrix_1.2-12
[15] DelayedArray_0.2.7 shiny_1.0.5
[17] parallel_3.5.0 gridExtra_2.3
[19] GenomeInfoDbData_0.99.0stringr_1.2.0
[21] UpSetR_1.3.3   S4Vectors_0.14.7
[23] IRanges_2.10.5 stats4_3.5.0
[25] MultiAssayExperiment_1.2.1 grid_3.5.0
[27] shinydashboard_0.6.1   glue_1.2.0
[29] Biobase_2.36.2 R6_2.2.2
[31] purrr_0.2.4tidyr_0.7.2
[33] magrittr_1.5   reshape2_1.4.2
[35] ggplot2_2.2.1  scales_0.5.0
[37] matrixStats_0.52.2 htmltools_0.3.6
[39] BiocGenerics_0.22.1GenomicRanges_1.28.6
[41] RaggedExperiment_1.0.0 SummarizedExperiment_1.6.5
[43] mime_0.5   xtable_1.8-2
[45] colorspace_1.3-2   httpuv_1.3.5
[47] stringi_1.1.6  RCurl_1.95-4.8
[49] lazyeval_0.2.1 munsell_0.4.3




On Wed, Dec 13, 2017 at 8:52 PM, Marcel Ramos <marcel.ra...@roswellpark.org>
wrote:

> Hi Maarten,
>
> It appears that your vignette is pointing to a package that doesn't exist
> in the build system.
>
> Please reference `package = "brgedata"` instead.
>
> Regards,
> Marcel
>
>
> *Note. Apologies if you've received this email twice.
>
> On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
>
> Dear all,
>
> Our new package, omicsPrint, has been accepted and added to the
> bioconductor build system but is not passing through on any system. Locally
> we are able to build install and execute the vignette. We have tried
> several things without success.
>
> The current error we got for version 0.99.29 on malbec2 is:
>
> Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics:
> parsing failed--expected only one '!series_data_table_begin'
>
> (https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
>
> )
>
> Anyone idea's or suggestions for debugging?
>
> Regards,
> Maarten and Davy
>
>   [[alternative HTML version deleted]]
>
> ___bioc-de...@r-project.org 
> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] unknown build error novel bioc. package

[Maarten van Iterson]

Dear all,

Our new package, omicsPrint, has been accepted and added to the
bioconductor build system but is not passing through on any system. Locally
we are able to build install and execute the vignette. We have tried
several things without success.

The current error we got for version 0.99.29 on malbec2 is:

Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics:
parsing failed--expected only one '!series_data_table_begin'

(
https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
)

Anyone idea's or suggestions for debugging?

Regards,
Maarten and Davy

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] adding multiple vignettes not all should be processed by the build-system

[Maarten van Iterson]

Dear all,

I've created a package that contains one vignette showing its core
functionality that I would like to be processed by the build-system and two
other vignettes showing more comprehensive examples, e.g. including
downloading publicly available data from GEO and 1000G vcfs which take too
much time and memory resources. I would like to show these two vignettes on
the landing page using prebuild html but don't want them to be processed by
the build-system.

Is this possible and if yes, what is the appropriate way to accomplish this?

The package is currently under review and called omicsPrint.

Regards,
Maarten

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

[Maarten van Iterson]

Thanks for the explanation and the proposed solution.
I was not aware the DelayedArray package was involved as well.
Maarten

On Fri, Apr 7, 2017 at 6:26 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:

> Hi Maarten, Vince,
>
> We need to fix this. The plan is to promote rowRanges to an S4 generic
> in the DelayedArray package (DelayedArray depends on matrixStats). And
> to remove the rowRanges S4 generic defined in SummarizedExperiment
> (SummarizedExperiment depends on DelayedArray). So we'll have only 1
> rowRanges generic (defined in DelayedArray). With methods defined in
> matrixStats (default method), DelayedArray (method for DelayedMatrix
> objects), and SummarizedExperiment (method for RangedSummarizedExperiment
> objects).
>
> Then there won't be anymore conflict.
>
> Will fix this ASAP.
>
> H.
>
>
>
> On 04/06/2017 03:11 AM, Vincent Carey wrote:
>
>> I am sure there are better responses to come, but here are a few initial
>> comments.
>>
>> On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson <mviter...@gmail.com>
>> wrote:
>>
>> Dear all,
>>>
>>> SummarizedExperiment and matrixStats both contain a method/function
>>> called
>>> rowRanges one operates on a SummarizedExperiment-object the other on a
>>> matrix. matrixStats is required by SummarizedExperiment, or a package it
>>> is
>>> depending on, so rowRanges is masked when loading SummarizedExperiment.
>>>
>>> I thought a function/method is called depended on the type of the object;
>>>
>>>
>> There are at least two interpretations of this.  If a function that is an
>> S3 generic is called on an entity whose class corresponds to an existing
>> method, that method will be invoked.  If a function that is an S4 generic
>> is called with (a sequence of) arguments corresponding to a method with
>> signature equivalent to the sequence of classes of the arguments, that
>> method will be invoked.  In matrixStats, rowRanges is just a first level
>> function, and will be invoked directly on anything that is passed -- e.g.,
>> rowRanges(4) is just an error, when matrixStats alone is loaded.
>>
>> matrix or SummarizedExperiment-object, such that functions/methods with
>> the
>>
>>> same name can coexist. However, this doesn't seems to work for rowRanges.
>>> The only way to access rowRanges from matrixStats when
>>> SummarizedExperiment
>>> is already loaded is using the double colon operator
>>> matrixStats::rowRanges. Is this intentional or is there a other way to
>>> solve this?
>>>
>>> Regards,
>>> Maarten
>>>
>>> Here is a small example showing the issue:
>>>
>>> library(SummarizedExperiment)
>>>>
>>> Loading required package: matrixStats
>>> matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats
>>> for
>>> help.
>>> Attaching package: ‘matrixStats’
>>> Attaching package: ‘SummarizedExperiment’
>>> The following object is masked from ‘package:matrixStats’:
>>> rowRanges
>>>
>>>> nrows <- 200; ncols <- 6
>>>> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
>>>> rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
>>>>
>>> +  IRanges(floor(runif(200, 1e5, 1e6)), width=100),
>>> +  strand=sample(c("+", "-"), 200, TRUE),
>>> +  feature_id=sprintf("ID%03d", 1:200))
>>>
>>>> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
>>>>
>>> +  row.names=LETTERS[1:6])
>>>
>>>> rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
>>>>
>>> + rowRanges=rowRanges, colData=colData)
>>>
>>>>
>>>> rowRanges(rse)
>>>>
>>> GRanges object with 200 ranges and 1 metadata column:
>>> seqnames   ranges strand |  feature_id
>>>   | 
>>> [1] chr1 [858613, 858712]  - |   ID001
>>>
>>>>
>>>> rowRanges(counts)
>>>>
>>> Error in (function (classes, fdef, mtable)  :
>>>   unable to find an inherited method for function ‘rowRanges’ for
>>> signature
>>> ‘"matrix"’
>>>
>>>>
>>>> library(matrixStats) ##it is already loading so this doesn't alter

[Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

[Maarten van Iterson]

Dear all,

SummarizedExperiment and matrixStats both contain a method/function called
rowRanges one operates on a SummarizedExperiment-object the other on a
matrix. matrixStats is required by SummarizedExperiment, or a package it is
depending on, so rowRanges is masked when loading SummarizedExperiment.

I thought a function/method is called depended on the type of the object;
matrix or SummarizedExperiment-object, such that functions/methods with the
same name can coexist. However, this doesn't seems to work for rowRanges.
The only way to access rowRanges from matrixStats when SummarizedExperiment
is already loaded is using the double colon operator
matrixStats::rowRanges. Is this intentional or is there a other way to
solve this?

Regards,
Maarten

Here is a small example showing the issue:

> library(SummarizedExperiment)
Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for
help.
Attaching package: ‘matrixStats’
Attaching package: ‘SummarizedExperiment’
The following object is masked from ‘package:matrixStats’:
rowRanges
> nrows <- 200; ncols <- 6
> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
> rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
+  IRanges(floor(runif(200, 1e5, 1e6)), width=100),
+  strand=sample(c("+", "-"), 200, TRUE),
+  feature_id=sprintf("ID%03d", 1:200))
> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
+  row.names=LETTERS[1:6])
> rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
+ rowRanges=rowRanges, colData=colData)
>
> rowRanges(rse)
GRanges object with 200 ranges and 1 metadata column:
seqnames   ranges strand |  feature_id
  | 
[1] chr1 [858613, 858712]  - |   ID001
>
> rowRanges(counts)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘rowRanges’ for signature
‘"matrix"’
>
> library(matrixStats) ##it is already loading so this doesn't alter the
search path
>
> rowRanges(rse)
GRanges object with 200 ranges and 1 metadata column:
seqnames   ranges strand |  feature_id
  | 
[1] chr1 [858613, 858712]  - |   ID001
> rowRanges(counts)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘rowRanges’ for signature
‘"matrix"’
>
> head(matrixStats::rowRanges(counts))
   [,1] [,2]
[1,]   51.27791 9350.048
[2,] 1417.41010 8272.040
> sessionInfo()
R Under development (unstable) (2016-08-25 r71150)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

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] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] SummarizedExperiment_1.5.7 DelayedArray_0.1.7
[3] matrixStats_0.51.0 Biobase_2.35.1
[5] GenomicRanges_1.27.23  GenomeInfoDb_1.11.10
[7] IRanges_2.9.19 S4Vectors_0.13.15
[9] BiocGenerics_0.21.3

loaded via a namespace (and not attached):
[1] lattice_0.20-34 bitops_1.0-6grid_3.4.0
[4] zlibbioc_1.21.0 XVector_0.15.2  Matrix_1.2-8
[7] RCurl_1.95-4.8  GenomeInfoDbData_0.99.0

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

[Maarten van Iterson]

Thanks for looking into this!

Maarten

On Mon, Apr 3, 2017 at 7:00 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:

> Hi Maarten,
>
> identical() is not reliable on DNAStringSet objects or other objects
> that contain external pointers as it can return false negatives as well
> as false positives. We'll fix the "cbind" and "rbind" methods for
> SummarizedExperiment to work around this problem.
>
> Thanks for the report.
>
> H.
>
>
> On 04/03/2017 12:58 AM, Maarten van Iterson wrote:
>
>> Dear list,
>>
>> Combining SummarizedExperiment object, containing a DNAStringSet in the
>> rowData seems not to work properly. If I cbind two SummarizedExperiment
>> objects, which I know are identical, an error is reported:
>>
>> Error in FUN(X[[i]], ...) (from #2) :
>>   column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not
>> match
>>
>> I think I traced the problem existing in `SummarizedExperiment:::.compa
>> re`
>> in that `identical` is used to compare DNAStringSets which is not behaving
>> as expected. Whereas it should return all identical it returns it is not!
>>
>> Here is a counter example (which was easier to construct) showing that
>> `identical` returns FALSE where it should return TRUE.
>>
>> library(Biostrings)
>>> seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>>> seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>>>
>>> seq1
>>>
>> [1] "GACTC"
>>
>>> seq2
>>>
>> [1] "GAATG"
>>
>>>
>>> s1 <- DNAStringSet(seq1)
>>> s2 <- DNAStringSet(seq2)
>>>
>>> str(s1)
>>>
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
>> with 2 slots
>>   .. .. ..@ xp_list:List of 1
>>   .. .. .. ..$ :
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :
>>   ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
>> with 7 slots
>>   .. .. ..@ group  : int 1
>>   .. .. ..@ start  : int 1
>>   .. .. ..@ width  : int 5
>>   .. .. ..@ NAMES  : NULL
>>   .. .. ..@ elementType: chr "integer"
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ metadata   : list()
>>   ..@ elementType: chr "DNAString"
>>   ..@ elementMetadata: NULL
>>   ..@ metadata   : list()
>>
>>> str(s2)
>>>
>> Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
>>   ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
>> with 2 slots
>>   .. .. ..@ xp_list:List of 1
>>   .. .. .. ..$ :
>>   .. .. ..@ .link_to_cached_object_list:List of 1
>>   .. .. .. ..$ :
>>
>>   ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
>> with 7 slots
>>   .. .. ..@ group  : int 1
>>   .. .. ..@ start  : int 1
>>   .. .. ..@ width  : int 5
>>   .. .. ..@ NAMES  : NULL
>>   .. .. ..@ elementType: chr "integer"
>>   .. .. ..@ elementMetadata: NULL
>>   .. .. ..@ metadata   : list()
>>   ..@ elementType: chr "DNAString"
>>   ..@ elementMetadata: NULL
>>   ..@ metadata   : list()
>>
>>>
>>> identical(seq1, seq2)
>>>
>> [1] FALSE
>>
>>> identical(s1, s2)
>>>
>> [1] TRUE
>>
>>> seq1 == seq2
>>>
>> [1] FALSE
>>
>>> s1 == s2
>>>
>> [1] FALSE
>>
>>>
>>> sessionInfo()
>>>
>> R version 3.3.2 (2016-10-31)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.2 LTS
>>
>> locale:
>>  [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
>>  [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
>>  [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
>>  [7] LC_PAPER=en_US.utf8   LC_NAME=C
>>  [9] LC_ADDRESS=C  LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats4stats graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] Biostrings_2.42.1  XVector_0.14.1
>>  [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4

[Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

[Maarten van Iterson]

Dear list,

Combining SummarizedExperiment object, containing a DNAStringSet in the
rowData seems not to work properly. If I cbind two SummarizedExperiment
objects, which I know are identical, an error is reported:

Error in FUN(X[[i]], ...) (from #2) :
  column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not match

I think I traced the problem existing in `SummarizedExperiment:::.compare`
in that `identical` is used to compare DNAStringSets which is not behaving
as expected. Whereas it should return all identical it returns it is not!

Here is a counter example (which was easier to construct) showing that
`identical` returns FALSE where it should return TRUE.

> library(Biostrings)
> seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
> seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>
> seq1
[1] "GACTC"
> seq2
[1] "GAATG"
>
> s1 <- DNAStringSet(seq1)
> s2 <- DNAStringSet(seq2)
>
> str(s1)
Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :
  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()
> str(s2)
Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :

  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()
>
> identical(seq1, seq2)
[1] FALSE
> identical(s1, s2)
[1] TRUE
> seq1 == seq2
[1] FALSE
> s1 == s2
[1] FALSE
>
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8   LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] Biostrings_2.42.1  XVector_0.14.1
 [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4.0
 [5] Biobase_2.34.0 GenomicRanges_1.26.4
 [7] GenomeInfoDb_1.10.3IRanges_2.8.2
 [9] S4Vectors_0.12.2   BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10 AnnotationDbi_1.36.2
hms_0.3
 [4] GenomicAlignments_1.10.1 zlibbioc_1.20.0
BiocParallel_1.8.1
 [7] BSgenome_1.42.0  lattice_0.20-35
R6_2.2.0
[10] httr_1.2.1   tools_3.3.2
grid_3.3.2
[13] DBI_0.6  assertthat_0.1
digest_0.6.12
[16] tibble_1.2   Matrix_1.2-8
readr_1.1.0
[19] rtracklayer_1.34.2   bitops_1.0-6
biomaRt_2.30.0
[22] RCurl_1.95-4.8   memoise_1.0.0
RSQLite_1.1-2
[25] compiler_3.3.2   GenomicFeatures_1.26.3
Rsamtools_1.26.1
[28] XML_3.98-1.5 jsonlite_1.3
VariantAnnotation_1.20.3
>

I don't completely understand understand why `identical` is not working
properly is it comparing the environment address in the above example they
are the same although the sequences are not? In my case the two
SummarizedExperiments contained the same DNAStringSets but had a different
environment address?

Regards,
Maarten

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Announcement of a new package called bacon

[Maarten van Iterson]

Dear list,

I would like to introduce the package bacon that has been added to
bioconductor just before the release of version 3.3.

bacon can be used to estimate and control for bias and inflation often
present in epigenome- and transcriptome-wide association
studies(EWAS/TWAS). The idea behind bacon is to estimate the empirical null
distribution from the data (using Bayesian statistics) and use the
empirical null i.s.o. a theoretical null for inference. Bacon supports
bias- and inflation-controlled fixed-effect meta-analysis that can be
executed in parallel. A manuscript is available from biorxiv (
http://biorxiv.org/content/early/2016/05/27/055772).

Kind regards,

Maarten van Iterson

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Maarten van Iterson]

Dear Dan and Henrik,

Thank you for looking into this!

So if I understand correctly the check error will disappear once the new
build/check reports has been generated.

Cheers,
Maarten

On Tue, Apr 12, 2016 at 3:00 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> Thanks for checking; minfi reads some (but not this exact one) of these
> IDATs as part of the build process.
>
> On Mon, Apr 11, 2016 at 8:18 PM, Henrik Bengtsson <
> henrik.bengts...@gmail.com> wrote:
>
>> No worries. Glad to hear it WS just a hiccup.
>>
>> Henrik
>> On Apr 11, 2016 4:53 PM, "Dan Tenenbaum" <dtene...@fredhutch.org> wrote:
>>
>> > I upgraded to r70462 and I cannot reproduce it now either. I guess it
>> was
>> > an issue in R-alpha, since fixed.
>> > Sorry for the trouble.
>> >
>> > Dan
>> >
>> >
>> > - Original Message -
>> > > From: "Henrik Bengtsson" <henrik.bengts...@gmail.com>
>> > > To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> > > Cc: "Maarten van Iterson" <mviter...@gmail.com>, "bioc-devel" <
>> > bioc-devel@r-project.org>
>> > > Sent: Monday, April 11, 2016 4:01:05 PM
>> > > Subject: Re: [Bioc-devel] moscato2 Windows build error reading IDAT
>> file
>> >
>> > > I *cannot* reproduce this:
>> > >
>> > > % R --vanilla
>> > > ## The IDAT file
>> > >> pathname <- system.file(package="minfiData", "extdata", "5723646053",
>> > >> "5723646053_R05C02_Grn.idat")
>> > >> file.info(pathname)$size
>> > > [1] 8091452
>> > >> unname(tools::md5sum(pathname))
>> > > [1] "dfc33fdaf3e91d872be896643a0c837f"
>> > >> packageVersion("minfiData")
>> > > [1] '0.13.0'
>> > >
>> > > ## Parsing it
>> > >> data <- illuminaio:::readIDAT_nonenc(pathname)
>> > >> str(data)
>> > > List of 12
>> > > $ fileSize : num 8091452
>> > > $ versionNumber: int 3
>> > > $ nFields  : int 19
>> > > $ fields   : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401
>> > 402 ...
>> > >  ..- attr(*, "dimnames")=List of 2
>> > >  .. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
>> > >  .. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
>> > > $ nSNPsRead: int 622399
>> > > $ Quants   : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
>> > > 1665 1953 5689 264 ...
>> > >  ..- attr(*, "dimnames")=List of 2
>> > >  .. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336"
>> ...
>> > >  .. ..$ : chr [1:3] "Mean" "SD" "NBeads"
>> > > $ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
>> > > 10600345 10600353 10600357 10600364 10600366 10600369 ...
>> > > $ RedGreen : int 0
>> > > $ Barcode  : chr "5723646053"
>> > > $ ChipType : chr "BeadChip 12x8"
>> > > $ RunInfo  : chr[0 , 1:5]
>> > >  ..- attr(*, "dimnames")=List of 2
>> > >  .. ..$ : NULL
>> > >  .. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
>> > > $ Unknowns :List of 7
>> > >  ..$ MostlyNull: chr ""
>> > >  ..$ MostlyA   : chr "R05C02"
>> > >  ..$ Unknown.1 : chr ""
>> > >  ..$ Unknown.2 : chr ""
>> > >  ..$ Unknown.3 : chr ""
>> > >  ..$ Unknown.4 : chr ""
>> > >  ..$ Unknown.5 : chr ""
>> > >
>> > >> sessionInfo()
>> > > R version 3.3.0 beta (2016-04-08 r70447)
>> > > Platform: x86_64-w64-mingw32/x64 (64-bit)
>> > > Running under: Windows 7 x64 (build 7601) Service Pack 1
>> > >
>> > > locale:
>> > > [1] LC_COLLATE=English_United States.1252
>> > > [2] LC_CTYPE=English_United States.1252
>> > > [3] LC_MONETARY=English_United States.1252
>> > > [4] LC_NUMERIC=C
>> > > [5] LC_TIME=English_United States.1252
>> > >
>> > > attached base packages:
>> > > [1] stats

[Bioc-devel] moscato2 Windows build error reading IDAT file

[Maarten van Iterson]

Dear all,

My package MethylAid does not pass check on moscato2.

I got

"Error in while (m%/%128 == 1) { : argument is of length zero
Calls: summarize ... readIDAT_nonenc -> lapply -> FUN -> readField ->
readString"

the summarize function calls read.metharray.exp from minfi which calls
readIDAT/readIDAT_nonenc
 from illuminaio. However, both packages do pass check on moscato2.

I don't know how to fix this or if the error is related to the new
windows toolchain?

Any idea's or suggestions are welcome!

Cheers,
Maarten

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Using Git with Bioconductor SVN repositories

[Maarten van Iterson]

Dear all,

I'm struggling with using git and the Bioconductor SVN repo of my packages.

For example, I have a package in devel (bacon) and managed to push changes
to the svn/trunk of my package using the steps described at:

https://www.bioconductor.org/developers/how-to/git-mirrors/

following scenario 2, but after

git checkout master
git merge devel

the decorate output of git log is:

*   e8e3752 - (HEAD, master) Merge branch 'devel' (22 seconds ago)

|\
| * fe340af - (git-svn-devel, devel) fix bug meta-analysis and add trimming
of test-statistics (in the future) 
* | 73921c7 - (origin/master, origin/HEAD) fix bug meta-analysis and add
trimming of test-statistics (15 minutes ago) 
|/
* 693fdba - (bioc/master) add ggplot versions of hist and qq add topTable
function and updating vignette (2 weeks ago) 
* fc2436f - update markdown file (2 weeks ago) 
* 52a7818 - add ggplot versions of hist and qq add topTable function and
updating vignette (2 weeks ago) 
* 92ed414 - fix typo and add URL and BugReports to DESCR. (2 weeks ago)

* b45332b - Adding doppelgangR, EpiCluster, PCAN, bacon, SwathXtend (3
weeks ago) 

whereas I expect every branch should be in sync.
The state of my fork is: 1 commit ahead, 1 commit behind
Bioconductor-mirror:master.  What should I do at this point?

If followed this scenario before and commit to git and push to GitHub as
normally but ended up in a state that I only could solve by removing my
fork from github and start all over again.

Cheers,
Maarten

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] not yet updated package sources/binaries in devel

[Maarten van Iterson]

Ok that is clear!
Thanks,
Maarten


On Thu, Mar 31, 2016 at 5:09 PM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:

> There were no windows build results yesterday, and Snow Leopard builds
> stopped some time ago. So nothing needs to be done.
> Dan
>
>
> - Original Message -----
> > From: "Maarten van Iterson" <mviter...@gmail.com>
> > To: "bioc-devel" <bioc-devel@r-project.org>
> > Sent: Thursday, March 31, 2016 12:01:04 AM
> > Subject: [Bioc-devel] not yet updated package sources/binaries in devel
>
> > Dear all,
> >
> > Should I worry about not yet updated package sources/binaries in devel:
> >
> > Package Source MethylAid_1.5.3.tar.gz
> > Windows Binary None
> > Mac OS X 10.6 (Snow Leopard) MethylAid_1.3.1.tgz
> > Mac OS X 10.9 (Mavericks) MethylAid_1.5.3.tgz
> >
> > For example, no binary for windows and old sources for Mac OS X 10.6.
> >
> > Whereas in release everything is in sync!
> >
> > Package Source MethylAid_1.4.0.tar.gz
> > Windows Binary MethylAid_1.4.0.zip
> > Mac OS X 10.6 (Snow Leopard) MethylAid_1.4.0.tgz
> > Mac OS X 10.9 (Mavericks) MethylAid_1.4.0.tgz
> >
> > Is this something I can fix?
> >
> > Kind regards,
> > Maarten
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] not yet updated package sources/binaries in devel

[Maarten van Iterson]

Dear all,

Should I worry about not yet updated package sources/binaries in devel:

Package Source MethylAid_1.5.3.tar.gz
Windows Binary None
Mac OS X 10.6 (Snow Leopard) MethylAid_1.3.1.tgz
Mac OS X 10.9 (Mavericks) MethylAid_1.5.3.tgz

For example, no binary for windows and old sources for Mac OS X 10.6.

Whereas in release everything is in sync!

Package Source MethylAid_1.4.0.tar.gz
Windows Binary MethylAid_1.4.0.zip
Mac OS X 10.6 (Snow Leopard) MethylAid_1.4.0.tgz
Mac OS X 10.9 (Mavericks) MethylAid_1.4.0.tgz

Is this something I can fix?

Kind regards,
Maarten

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel