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] warning on href

[Aimin Yan]

I got this warning when I perform CRAN check on my package


* checking Rd files ... WARNING

gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL

problem found in ‘gmtGene2Cat.Rd’



Here is my code for this Rd

@details This function reads a gene set file in \href{
https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29}{GMT
format}, and returns a list with its name being a gene id, and each element
of ...



I did not get this warning when I perform BiocCheck on my package.


Does anyone has an idea on how to fix this?


Thank you,


Aimin

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Re: [Bioc-devel] Bioconductor stats

[Sean Davis]

On Tue, Jun 27, 2017 at 7:34 AM, Lluís Revilla 
wrote:

> Hi,
>
> I have been looking at the stats of Bioconductor, and I would like to know
> more about how are they calculated.
>
> Do these stats account for the mirror sites? Are there any stats of the
> usage of mirrors?
>

Mirrors are not counted.


>
> I found some packages that for the same month they have downloads in two
> categories. For instance AnnotationDbi has some downloads as experimental
> data package:
> http://bioconductor.org/packages/stats/data-experiment/AnnotationDbi/
> while
> most of the downloads are in the software category (The right one). It
> seems that near 500 packages have downloads in two categories.
>

I'm not sure on this one.


>
> The "Nb of distinct IPs" if I understand correctly is for each package and
> month. So if the same IP downloads again the package is listed as a new IP,
> isn't it? I assume that if mirrors are counted either no one downloads the
> same packages from different mirrors in the same IP or that these
> information is shared across mirrors for these stats.
>

Again, mirrors are not included. I think the distinct IPs are reset per
month for the monthly stats.


>
> Regards,
>
> Lluís
>
> [[alternative HTML version deleted]]
>
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-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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[Bioc-devel] Bioconductor stats

[Lluís Revilla]

Hi,

I have been looking at the stats of Bioconductor, and I would like to know
more about how are they calculated.

Do these stats account for the mirror sites? Are there any stats of the
usage of mirrors?

I found some packages that for the same month they have downloads in two
categories. For instance AnnotationDbi has some downloads as experimental
data package:
http://bioconductor.org/packages/stats/data-experiment/AnnotationDbi/ while
most of the downloads are in the software category (The right one). It
seems that near 500 packages have downloads in two categories.

The "Nb of distinct IPs" if I understand correctly is for each package and
month. So if the same IP downloads again the package is listed as a new IP,
isn't it? I assume that if mirrors are counted either no one downloads the
same packages from different mirrors in the same IP or that these
information is shared across mirrors for these stats.

Regards,

Lluís

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[Bioc-devel] Deprecating a class

[Carlos Ruiz]

Hi Bioc developers,

A year ago, we introduced a class in my package MEAL to manage 
methylation data. After some Bioc releases, we realised that we don't 
really need this class and that it is better to reuse other Bioc classes 
to facilitate package usability. Is there any protocol to deprecate a 
class? There is only a guide to deprecate functions and methods.


For the new release, I was thinking on deprecating the constructors of 
my class, while keeping the methods. Is that OK?


Bests,

--
Carlos Ruiz
PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus MAR
Barcelona Biomedical Research Park (PRBB) (office 001)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 7309
carlos.r...@isglobal.org
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