[Bioc-devel] Bioc 3.7 build failed for GenvisR package

[Zach Skidmore]

Hi All,

I've noticed GenVisR is failing to build the vignette on windows for 
bioc-devel. the error seems to be:

"Invalid Parameter - /figure-html"



This seems like it may be related to the use of BiocStyle given this post on 
stackoverflow: 
https://stackoverflow.com/questions/48747959/biocstyle-vignettes-invalid-parameter-figure-html.

Has anyone encountered this before? I found a thread on here from 10/19/17 
which seems related but appeared to be resolved and there are not massive 
package failures for yesterday so I'm a bit confused as to what the actual 
issue is. I suppose I could set the output to .pdf instead of .html and see if 
that helps.

Any thoughts or suggestions are appreciated

Zach




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[Bioc-devel] writing unit tests for functions in an initializer

[Zach Skidmore]

Hi All,

I maintain the GenVisR package and am currently converting it to S4 classes. 
I'm running into a problem however when writing unit tests for functions within 
the initalizer. What I really need is a "mock" object of the class for which 
the initializer unit tests are being performed but which hold no data. This 
will allow me to step through the initializer "sub functions" and write tests 
for each one. The problem is I don't see a way in the S4 system to create a 
mock object. I've found this post that will do what I want 
http://r.789695.n4.nabble.com/Using-a-mock-of-an-S4-class-td4728547.html, 
however when using this solution R CMD CHECK throws errors:

* checking dependencies in R code ... WARNING
Unexported object imported by a ':::' call: ‘methods:::C_new_object’
  See the note in ?`:::` about the use of this operator.
  Including base/recommended package(s):
  ‘methods’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call to a base package:
  .Call(methods:::C_new_object, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.

I'm wondering if anyone has any ideas on the best way to handle this. I suppose 
i could create a "test" flag within the initalizer that would create an empty 
object of that class and use that but it seems hacky to do this.

thanks!
Zach


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[Bioc-devel] Problems with updating release branch

[Zach Skidmore]

Hi All,

On Monday I pushed a few documentation/bug updates to  RELEASE_3_5 from these 
remotes:

bioc
g...@git.bioconductor.org:packages/GenVisR.git
 (fetch)
bioc
g...@git.bioconductor.org:packages/GenVisR.git
 (push)

However these changes still have not shown up, pulling the release branch I can 
see the version is 1.6.1 however on the genvisr landing page 
https://bioconductor.org/packages/release/bioc/html/GenVisR.html I see the 
version is still 1.6.0

Any ideas what's going on, I would have thought these would have showed up 
yesterday

Zach


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Re: [Bioc-devel] check returns error on multiple dependent functions

[Zach Skidmore]

The collate field in the description file might help. It will control the order 
in which files are loaded I would imagine this would also alter the order 
examples are run in but I can not say with 100% certainty.

Zach

On 6/27/17 4:19 PM, Arman Sh wrote:


I’m developing  a package in which there are multiple functions that are 
dependent to each other. I have saved the functions in separate R files. When I 
run functions in correct order, I can easily get the output, but cmd check 
returns error. How can I prevent the error?

Best regards,
Arman



==> devtools::check()

Updating cbaf documentation
Loading cbaf
Loading required package: cgdsr
Loading required package: xlsxjars
Loading required package: rJava
Loading required package: xlsx
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

lowess

Loading required package: RColorBrewer
Loading required package: rafalib
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:rJava':

anyDuplicated, duplicated, sort, unique

The following objects are masked from 'package:stats':

IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Setting env vars --
CFLAGS  : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building cbaf -
"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD build "Z:\cbaf\Source code\cbaf" --no-resave-data  \
  --no-manual

* checking for file 'Z:\cbaf\Source code\cbaf/DESCRIPTION' ... OK
* preparing 'cbaf':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'cbaf_0.99.0.tar.gz'

Setting env vars --
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking cbaf -
"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD check  \
  "C:\Users\Arman\AppData\Local\Temp\RtmpoZ2dZa/cbaf_0.99.0.tar.gz" --as-cran  \
  --timings --no-manual

* using log directory 'Z:/cbaf/Source code/cbaf.Rcheck'
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'cbaf/DESCRIPTION' ... OK
* this is package 'cbaf' version '0.99.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'cgdsr' 'xlsxjars' 'xlsx' 'gplots' 'RColorBrewer' 'rafalib' 'Biobase'
  'genefilter'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cbaf' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... 

[Bioc-devel] Passing packages as variables?

[Zach Skidmore]

Hi all,

I maintain the GenVisR package. I am currently working on an update to provide 
support for VEP, the problem is I need to grab the reference sequence for 
locations in the VEP file. I know how to do this with BSgenome however within 
the package methods I need to figure out a way to load the genome package to 
get the references. The problem is this genome package can change based on the 
information in the VEP header. I could do something like this:

genome <- findCorrectGenome()
library(genome, character.only=T)
refBases <- getSeq(genome, Granges)
detach(genome, unload = T, character.only = T)

It feels wrong to have library calls like this within the package though. As an 
alternative I suppose I could put in the suggests field all BSgenome packages, 
but I don't really want to do that either. does any one have a better idea? I 
think the ideal solution would be to just do something like this:

refBases <- getSeq(geome::genome, Granges)

But i have no idea if it's even possible to pass variables as package names 
like this. As a last resort I could make a user just supply the correct 
BSgenome object but I would rather GenVisR be nice and use the correct one 
corresponding to the vep header without any user input if possible. Any help or 
advice is appreciated!

Thanks!

Zach


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[Bioc-devel] SVN E155000 GenVisR package

[Zach Skidmore]

Hi All,

I am trying to patch a bug on the release branch for the GenVisR package, 
however I can't seem to checkout the release branch:

svn co 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GenVisR
svn: E155000: '/Users/zskidmor/bioconductor/SVN/GenVisR' is already a working 
copy for a different URL

I tried blowing away the entire repo on my local machine and re-cloning it 
however I still get the same error when trying to switch to the release branch. 
I also noticed that I can't even view the files on hedgehog, when I try to go 
to either 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GenVisR
 or https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenVisR I get 
an "internal server error" I don't know if that is related or not?

Apologies if the answer is obvious, i'm much more familiar with git.

Zach


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Re: [Bioc-devel] S4 overwrite inspector of virtual class

[Zach Skidmore]

maybe validator is the proper term in R? i've highlighted what I refer to as 
the inspector below as an example:

setClass("file",
contains="file_virtual",
validity=function(object){
# Check that object is as expected

}
)

On 8/15/16 11:46 AM, Gabe Becker wrote:

Zach,

Is an inspector a method you define on your classes? I'm not quite
following what you mean by your question. AFAIK inspectors are not
generally a thing in R (at least that go by that name).

~G

On Mon, Aug 15, 2016 at 9:42 AM, Zach Skidmore 
<zskid...@wustl.edu><mailto:zskid...@wustl.edu> wrote:



Hi All,

I'm currently transforming the GenVisR package into an Object Oriented
system. Currently I have a virtual class and several child-classes. I am
wondering if there is a way to tell R to use the inspector of the virtual
class only if the inspector of a child class in not defined.

For example say I had a class to store versions of a file-type and I have
a slot in the class to store the position. Between different versions of
the file-type there may be small differences (for example Chromosome may be
capitalized in version 2,3,4 but not version 1). Ideally the child classes
for 2,3,4 would be able to inherit the inspector from the virtual class to
check the chromosome name and I would define a separate inspector for
version 1 which is different.

Any thoughts? Currently both inspectors are called (virtual and the
appropriate sub-class), meaning if i added more versions in the future I
would have to re-write the virtual and child class. Whereas if I could say
ignore the virtual (i.e. default) inspector if another is defined I would
only have to write the child class inspector in the future.

Hopefully this makes sense, let me know if it doesn't or if i'm violating
a core OO principle, i'm relatively new to object oriented programming.

Thanks, Zach!


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[Bioc-devel] S4 overwrite inspector of virtual class

[Zach Skidmore]

Hi All,

I'm currently transforming the GenVisR package into an Object Oriented system. 
Currently I have a virtual class and several child-classes. I am wondering if 
there is a way to tell R to use the inspector of the virtual class only if the 
inspector of a child class in not defined.

For example say I had a class to store versions of a file-type and I have a 
slot in the class to store the position. Between different versions of the 
file-type there may be small differences (for example Chromosome may be 
capitalized in version 2,3,4 but not version 1). Ideally the child classes for 
2,3,4 would be able to inherit the inspector from the virtual class to check 
the chromosome name and I would define a separate inspector for version 1 which 
is different.

Any thoughts? Currently both inspectors are called (virtual and the appropriate 
sub-class), meaning if i added more versions in the future I would have to 
re-write the virtual and child class. Whereas if I could say ignore the virtual 
(i.e. default) inspector if another is defined I would only have to write the 
child class inspector in the future.

Hopefully this makes sense, let me know if it doesn't or if i'm violating a 
core OO principle, i'm relatively new to object oriented programming.

Thanks, Zach!


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[Bioc-devel] System Requirements for imported packages

[Zach Skidmore]

Hi All,

I'm curious what the preferred method is for dealing with System 
Requirements originating from an imported package. For example, if I had 
a package that imported `biomaRt` which itself imports `XML` which has 
the SystemRequirement `libxml2` how is that dealt with? Are package 
installers expected to troubleshoot this (via install messages), should 
I put this requirement and install instructions for `libxml2` in a 
README for my package?


Thanks for any input,
Zach

--
Zachary L. Skidmore
Staff Scientist
McDonnell Genome Institute
Washington University in Saint Louis



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[Bioc-devel] Unit tests present/ coverage "unknown"

[Zach Skidmore]

Hi All,

Maybe i'm missing something but I don't quite understand why the "test 
coverage" badge on the GenVisR page displays unknown. I have unit tests 
set up with testthat, and looking at the  R CMD CHECK reports I see that 
they are running however the badge still reads as "unknown". Any Ideas? 
I have looked through the bioc devel pages to no avail, I assume I have 
to set a flag somewhere.


Thanks!
Zach

--
Zachary L. Skidmore
Staff Scientist
McDonnell Genome Institute
Washington University in Saint Louis



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[Bioc-devel] GenVisR vignette build issues

[Zach Skidmore]

Hi All,

Recently the vignette in the GenVisR package has been causing Check 
Errors, Specifically the error is:

pandoc: Could not fetch /tabsets.js
/tabsets.js: openBinaryFile: does not exist (No such file or directory)
Error: processing vignette 'GenVisR_intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted

I cannot reproduce the error on my local system, some searching suggests 
that the problem might be with rmarkdown however I have the latest 
version installed. Is there anyway to tell what version Bioc is using?

Zach

-- 
Zachary L. Skidmore
Staff Scientist
McDonnell Genome Institute
Washington University in Saint Louis




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[Bioc-devel] GenVisR Release

[Zach Skidmore]

GenVisR is now available for use on the devel branch.

GenVisR Is designed to produce highly customizable graphical 
representations of genomic sequence data, focused primarily on 
cohort-level visuals. Visuals fall into three broad categories, "small 
variants" (snvs/indels), sturcutral variation (copy number alteration, 
loss of heterozygosity), and data quality visuals. Bug reports and 
feature requests can be submitted to 
https://github.com/griffithlab/GenVisR/issues


Best,
Zach

--
Zachary L. Skidmore
Staff Scientist
McDonnell Genome Institute
Washington University in Saint Louis



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