Re: [Bioc-devel] exonsBy dropping genes from TxDb

2017-10-27 Thread Hervé Pagès 

The problem seems to originate in the BioMart service itself:

  library(biomaRt)
  mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

  attributes1 <- c("ensembl_transcript_id", "ensembl_exon_id")
  df1 <- getBM(attributes1, mart=mart)

  dim(df1)
  # [1] 1150974   2

  subset(df1, ensembl_transcript_id == "ENST0485971")
  # ensembl_transcript_id ensembl_exon_id
  # 1078905   ENST0485971 ENSE1952391
  # 1078906   ENST0485971 ENSE3639486
  # 1078907   ENST0485971 ENSE1881546

Correct. ENST0485971 has 3 exons.

But if I request more attributes:

  attributes2 <- c(attributes1, "rank", "genomic_coding_start", 
"cds_start", "5_utr_start")

  df2 <- getBM(attributes2, mart=mart)

  dim(df2)
  # [1] 1051158   6

Uh, less rows?

  subset(df2, ensembl_transcript_id == "ENST0485971")
  # [1] ensembl_transcript_id ensembl_exon_id   rank
  # [4] genomic_coding_start  cds_start 5_utr_start
<0 rows> (or 0-length row.names)

ENST0485971 disappeared from the result!

It's like someone replaced a LEFT JOIN with an INNER JOIN somewhere
in the BioMart service.

The impact of this on makeTxDbFrombiomart() is that many exons indeed
don't make it into the TxDb object so we end up with many exon-less
transcripts. I'll add a sanity check and will error when this happens. 
Better fail with an informative error message than silently return

a broken TxDb.

Before I contact the BioMart people about this, I'd like to remove R
and the biomaRt package from the equation but I'm not sure how to do
that (I was not able to reproduce the problem by using their web
interface https://www.ensembl.org/biomart). Any help with this would
be greatly appreciated.

Thanks,
H.

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/hpages/R/R-3.4.2-bioc35/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.4.2-bioc35/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] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] biomaRt_2.32.1   BiocInstaller_1.26.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13 IRanges_2.10.5   XML_3.98-1.9
 [4] digest_0.6.12bitops_1.0-6 DBI_0.7
 [7] stats4_3.4.2 RSQLite_2.0  rlang_0.1.2
[10] blob_1.1.0   S4Vectors_0.14.7 tools_3.4.2
[13] bit64_0.9-7  Biobase_2.36.2   RCurl_1.95-4.8
[16] bit_1.1-12   parallel_3.4.2   compiler_3.4.2
[19] BiocGenerics_0.22.1  AnnotationDbi_1.38.2 memoise_1.1.0
[22] tibble_1.3.4


On 10/27/2017 10:05 AM, Hervé Pagès wrote:

Hi Leonard,

Sorry for missing your earlier posts about this. Will look into it.

Thanks,
H.

On 10/27/2017 09:07 AM, Leonard Goldstein wrote:

Dear bioc-devel,

I noticed exonsBy is dropping a lot of genes when run on a TxDb object
created with makeTxDbFromBiomart (see below). Please also see related
post
on the Bioconductor support site:

https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_101951_-23102160=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ExVvVr6r4wUKgBmPNOQiJXSI2O1FYqFRz_llKQY_jD0=xUz41e2CIjMTXmO5LqkFp12ySvH9zzA0s5OMWzgWosU=


Thanks for your help.

Leonard

--

tx <- makeTxDbFromBiomart()
txs_by_gene <- transcriptsBy(tx, "gene")
exs_by_gene <- exonsBy(tx, "gene")
length(txs_by_gene)

[1] 63967

length(exs_by_gene)

[1] 36751

subsetByOverlaps(txs_by_gene, GRanges("8",
IRanges(127735434,127741434)))

GRangesList object of length 1:
$ENSG0136997
GRanges object with 9 ranges and 2 metadata columns:
   seqnames ranges strand | tx_id tx_name
   |  
   [1]8 [127735434, 127740477]  + |101876 ENST0259523
   [2]8 [127735473, 127735817]  + |101877 ENST0641252
   [3]8 [127735519, 127738772]  + |101878 ENST0517291
   [4]8 [127736046, 127736612]  + |101879 ENST0641036
   [5]8 [127736069, 127741434]  + |101880 ENST0621592
   [6]8 [127736084, 127741434]  + |101881 ENST0377970
   [7]8 [127736220, 127741372]  + |101882 ENST0524013
   [8]8 [127736231, 127738475]  + |101883 ENST0520751
   [9]8 [127736594, 127740958]  + |101884 ENST0613283

---
seqinfo: 555 sequences (1 circular) from an unspecified genome

subsetByOverlaps(exs_by_gene, GRanges("8",
IRanges(127735434,127741434)))

GRangesList object of length 0:
<0 elements>

---
seqinfo: 555

Re: [Bioc-devel] possible bug in Rhtslib::pkgconfig

2017-10-27 Thread Aaron Lun 
The "Re:" in the title of this e-mail? I add an "Re:" to all my titles,
and I assume that the mailing list dispatcher adds the "[Bioc-devel]"
tag (cleverly inserting it between the "Re:" and the actual title).

Just looked it up - apparently it stands for "in re" in Latin. I guess I
learn something new every day.

Martin Morgan wrote:
> Thanks Aaron I'll follow up on the support site.
>
> Can you clarify where the 'Re:' came from in the title? I can't find a
> previous post with similar title.
>
> Martin
>
> On 10/27/2017 05:42 AM, Aaron Lun wrote:
>> Dear list,
>>
>> It seems that there is an issue with Rhtslib::pkgconfig() regarding the
>> identification of the location of the shared library on some systems:
>>
>> https://support.bioconductor.org/p/102248/
>>
>> To summarize: on this system, R is putting the shared library in lib64/,
>> while pkgconfig() looks for it in lib/. This results in linkage errors
>> for all packages depending on Rhtslib on this system. I imagine that the
>> same would happen for all library packages, e.g., beachmat, Rhdf5lib.
>>
>> Looking at the Makevars for Rhtslib suggests that the shared library is
>> stored in ${R_PACKAGE_DIR}/lib${R_ARCH}, while pkgconfig only ever looks
>> in lib/. I assume that this usually works because ${R_ARCH} is empty on
>> most linux systems, though perhaps this cannot be guaranteed.
>>
>> Cheers,
>>
>> Aaron
>> ___
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>>
>
>
> This email message may contain legally privileged and/or confidential
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Re: [Bioc-devel] rcellminer Bioconductor package

2017-10-27 Thread Elloumi, Fathi (NIH/NCI) [C] 
Hi Nitesh,

I started merging and updating package rcellminerData following the 
instructions here : 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

I have conflict merge in step 7:
git merge --allow-unrelated-histories upstream/master

warning: Cannot merge binary files: data/molData.RData (HEAD vs. 
upstream/master)
warning: Cannot merge binary files: data/drugData.RData (HEAD vs. 
upstream/master)
Auto-merging inst/extdata/CellLineToOncoTree.txt
CONFLICT (add/add): Merge conflict in inst/extdata/CellLineToOncoTree.txt
Auto-merging data/molData.RData
CONFLICT (add/add): Merge conflict in data/molData.RData
Auto-merging data/drugData.RData
CONFLICT (add/add): Merge conflict in data/drugData.RData
Auto-merging NAMESPACE
CONFLICT (add/add): Merge conflict in NAMESPACE
Auto-merging DESCRIPTION
CONFLICT (add/add): Merge conflict in DESCRIPTION
Automatic merge failed; fix conflicts and then commit the result.

$git status
On branch master
Your branch is up-to-date with 'origin/master'.
You have unmerged paths.
  (fix conflicts and run "git commit")
  (use "git merge --abort" to abort the merge)

Changes to be committed:

new file:   data/datalist
new file:   external_data_store.txt
new file:   inst/extdata/make_rcellminerdata.R
new file:   inst/tests/test_rcellminerData.R
new file:   tests/runTests.R

Unmerged paths:
  (use "git add ..." to mark resolution)

both added:  DESCRIPTION
both added:  NAMESPACE
both added:  data/drugData.RData
both added:  data/molData.RData
both added:  inst/extdata/CellLineToOncoTree.txt

I was able to edit files DESCRIPTION and NAMESPACE and solve the conflict 
however it is not DOABLE for data files (*.txt and .Rdata) to make edit and 
remove undesirable parts. 

I want to check that the solution is to run:

git checkout –ours data/drugData.RData
git checkout –ours data/molData.RData
git checkout –ours inst/extdata/CellLineToOncoTree.txt

git add *
git commit

and then step 9

Another question: should I go through step 10 for RELEASE_3_5 (what about the 
others 3_1 to 3_4).  Please advise.

Best,

-- Fathi
 
Fathi Elloumi, PhD
Bioinformatics Software Engineer 
Contractor CSRA
Developmental Therapeutics Branch
NIH/NCI/CCR
Phone: 240-760-6601
 

Here are my remotes:
origin  https://github.com/CBIIT/rcellminerData.git (fetch)
origin  https://github.com/CBIIT/rcellminerData.git (push)
upstreamg...@git.bioconductor.org:packages/rcellminerData.git (fetch)
upstreamg...@git.bioconductor.org:packages/rcellminerData.git (push)



On 10/10/17, 10:25 AM, "Turaga, Nitesh"  wrote:

You should have access if you have submitted the new key.

We suggest your link your GitHub ID. And add keys to your Github, and we 
can get them from there. If you have submitted your GitHub ID once to the 
google form, you won’t have to resubmit. 

Best,

Nitesh 


> On Oct 7, 2017, at 9:04 AM, Elloumi, Fathi (NIH/NCI) [C] 
 wrote:
> 
> Hi Nitesh,
> 
> I added a new ssh key to allow access from Laptop. Could you grant me 
permission  for my 2 ssh keys?
> 
> Thanks.
> 
> Fathi
> 



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
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Re: [Bioc-devel] issues with access to my Bioconductor repository IntramiRExploreR

2017-10-27 Thread Turaga, Nitesh 
We have the following public key in our system

ssh-rsa 
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

This is the one you submitted to the google form, and this is the one that was 
added.

If you want to link your GitHub ID you have to resubmit to the google form.

Best,

Nitesh 


> On Oct 27, 2017, at 3:36 PM, Surajit Bhattacharya 
>  wrote:
> 
> Thanks Lori. The problem still persists.
> 
> $ git remote add upstream 
> g...@git.bioconductor.org:packages/IntramiRExploreR.git
> $ git fetch upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> 
> I have the ssh keys updated in my github account, still the problem persists. 
> Can you guide me regarding the same.
> 
> 
> Thanks,
> 
> Surajit
> 
> 
> From: Shepherd, Lori 
> Sent: Friday, October 27, 2017 7:40:08 AM
> To: Surajit Bhattacharya; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] issues with access to my Bioconductor repository 
> IntramiRExploreR
> 
> 
> Hello,
> 
> 
> It looks like when you submitted your package we were still in svn and had 
> provided a svn id that was associated with your package. This was the id that 
> we would have originally requested in the form for rsa keys.
> 
> 
> We have changed the id on our system to match your github id and you should 
> have access now.
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Cancer Institute
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Bioc-devel  on behalf of Surajit 
> Bhattacharya 
> Sent: Thursday, October 26, 2017 6:11:18 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] issues with access to my Bioconductor repository 
> IntramiRExploreR
> 
> Hello,
> 
> 
> I was trying to make some final changes to my package yesterday (changing the 
> README file with the link to the bioconductor page, instead of my github 
> repository), but am getting errors in accessing the bioconductor repository.
> 
> I followed the flow given in the webpage:
> 
> 
> ##Added the bioconductor git
> 
> $ git remote add upstream 
> g...@git.bioconductor.org:packages/IntramiRExploreR.git
> 
> ##Fetching from upstream
> 
> $ git fetch upstream
> 
> Permission denied (publickey).
> 
> fatal: Could not read from remote repository.
> 
> 
> 
> Please make sure you have the correct access rights
> 
> and the repository exists.
> 
> ##Remote -v
> 
> $ git remote -v
> 
> origin  
> https://github.com/sbhattacharya3/IntramiRExploreR.git
>  (fetch)
> 
> origin  
> https://github.com/sbhattacharya3/IntramiRExploreR.git
>  (push)
> 
> upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git 
> (fetch)
> 
> upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git (push)
> 
> 
> I have added my public key to the bioconductor list earlier as told then. Can 
> you please guidre me regarding the same.
> 
> 
> Thanks,
> 
> Surajit
> 
> 
> 
>[[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
>

Re: [Bioc-devel] issues with access to my Bioconductor repository IntramiRExploreR

2017-10-27 Thread Surajit Bhattacharya 
Thanks Lori. The problem still persists.

$ git remote add upstream 
g...@git.bioconductor.org:packages/IntramiRExploreR.git
$ git fetch upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


I have the ssh keys updated in my github account, still the problem persists. 
Can you guide me regarding the same.


Thanks,

Surajit


From: Shepherd, Lori 
Sent: Friday, October 27, 2017 7:40:08 AM
To: Surajit Bhattacharya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] issues with access to my Bioconductor repository 
IntramiRExploreR


Hello,


It looks like when you submitted your package we were still in svn and had 
provided a svn id that was associated with your package. This was the id that 
we would have originally requested in the form for rsa keys.


We have changed the id on our system to match your github id and you should 
have access now.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Surajit 
Bhattacharya 
Sent: Thursday, October 26, 2017 6:11:18 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] issues with access to my Bioconductor repository 
IntramiRExploreR

Hello,


I was trying to make some final changes to my package yesterday (changing the 
README file with the link to the bioconductor page, instead of my github 
repository), but am getting errors in accessing the bioconductor repository.

I followed the flow given in the webpage:


##Added the bioconductor git

$ git remote add upstream 
g...@git.bioconductor.org:packages/IntramiRExploreR.git

##Fetching from upstream

$ git fetch upstream

Permission denied (publickey).

fatal: Could not read from remote repository.



Please make sure you have the correct access rights

and the repository exists.

##Remote -v

$ git remote -v

origin  
https://github.com/sbhattacharya3/IntramiRExploreR.git
 (fetch)

origin  
https://github.com/sbhattacharya3/IntramiRExploreR.git
 (push)

upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git (fetch)

upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git (push)


I have added my public key to the bioconductor list earlier as told then. Can 
you please guidre me regarding the same.


Thanks,

Surajit



[[alternative HTML version deleted]]

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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.

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Re: [Bioc-devel] FW: Package build error

2017-10-27 Thread Hervé Pagès 

On 10/27/2017 11:42 AM, Ioannis Vardaxis wrote:

Hey,


I think the problem might be coming from the command
"file.path(path.expand('~'),'Desktop’)” on line 77 on MACPET.rmd file. I
just want to find the desktop path for creating a folder there for the
vignette and the examples. This seems to work on MAC, but not on the other
platforms, how can I make it work in general?


Please don't assume that all your users are going to have a
~/Desktop folder.

If you just need a place to create temporary files, you should use
tempfile().

BTW those are not Bioconductor specific questions and are better asked
on r-help or SO.

Thanks,
H.



I replaced pdf_document2 with pdf_document by the way.


Best,



--
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] FW: Package build error

2017-10-27 Thread Ioannis Vardaxis 
Hey,


I think the problem might be coming from the command
"file.path(path.expand('~'),'Desktop’)” on line 77 on MACPET.rmd file. I
just want to find the desktop path for creating a folder there for the
vignette and the examples. This seems to work on MAC, but not on the other
platforms, how can I make it work in general?

I replaced pdf_document2 with pdf_document by the way.


Best,

-- 
Ioannis Vardaxis

Stipendiat IMF
NTNU




On 27/10/2017, 20:08, "Bioc-devel on behalf of Ioannis Vardaxis"

wrote:

>Hey,
>
>Here is the report:
>
>bioconductor.org/spb_reports/MACPET_buildreport_20171027135637.html
>
>I get a warning for Warning: No Rd macros in package ‘Rdpack’, for which
>I can’t find any solution in the internett. But I am guessing that the
>warning might come from a special norwegian character Ø in the Rd files.
>I just write Ø in the documentation, because \o did not work . Do you
>think the problem is that?
>
>
>Furthermore, I get an error for the vignette. On mac it works fine (I
>work on mac too), but on the other two platforms a get:
>
>
>  *
>
>creating vignettes ...Warning: running command
>'"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla
>--default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"'
>had status 1
> ERROR
>Warning: 'pdf_document2' is deprecated.
>Use 'pdf_document' instead.
>
>Also :
>
>Error: processing vignette 'MACPET.Rmd' failed with diagnostics:
>
>savedir does not exist!
>
>However I am not getting any such error on my mac so it is quite
>difficult to find out how they are caused.
>
>Best,
>--
>Ioannis Vardaxis
>Stipendiat IMF
>NTNU
>
>From: "Shepherd, Lori"
>>
>Date: Friday, 27 October 2017 at 19:44
>To: Ioannis Vardaxis
>>, Hervé Pagès
>>,
>"bioc-devel@r-project.org"
>>
>Subject: Re: [Bioc-devel] FW: Package build error
>
>
>Make sure your webhook is set up as described
>
> 
>https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#
>adding-a-web-hook
>
>You will need to bump the version in the description file each time you
>would like a new build report so please make the bump from 0.99.0 to
>0.99.1.  Thank you.
>
>
>
>Lori Shepherd
>
>Bioconductor Core Team
>
>Roswell Park Cancer Institute
>
>Department of Biostatistics & Bioinformatics
>
>Elm & Carlton Streets
>
>Buffalo, New York 14263
>
>
>From: Bioc-devel 
>
>> on behalf of Ioannis Vardaxis
>>>
>Sent: Friday, October 27, 2017 1:22:26 PM
>To: Hervé Pagès; bioc-devel@r-project.org
>Subject: Re: [Bioc-devel] FW: Package build error
>
>Hey,
>
>One quick question. When I push again now, do I need to change the version
>from 0.99.0 to 0.99.1 or does it change automatically?
>
>Best,
>--
>Ioannis Vardaxis
>
>Stipendiat IMF
>NTNU
>
>
>
>
>On 27/10/2017, 19:03, "Hervé Pagès"
>> wrote:
>
>>Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
>>
>>hpages@latitude:~/MACPET$ git diff
>>diff --git a/DESCRIPTION b/DESCRIPTION
>>index d8238b6..061d692 100644
>>--- a/DESCRIPTION
>>+++ b/DESCRIPTION
>>@@ -7,6 +7,7 @@ Author: Ioannis Vardaxis
>>  Maintainer: Ioannis Vardaxis
>>>
>>  Description: The MACPET package can be used for binding site analysis
>>for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM for
>>  License: GPL-3
>>+SystemRequirements: C++11
>>  Encoding: UTF-8
>>  LazyData: true
>>  ByteCompile: true
>>
>>
>>hpages@latitude:~$ Rbiocdev CMD INSTALL MACPET
>>* installing to library '/home/hpages/R/R-3.4.2-bioc36/library'
>>* installing *source* package 'MACPET' ...
>>** libs
>>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>>-I/usr/local/include   -fpic  -g -O2 -c
>>PeakFinderSubFunctions_SGT_Rcpp.cpp -o PeakFinderSubFunctions_SGT_Rcpp.o
>>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>>-I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
>>g++ -std=gnu++11 -shared -L/home/hpages/R/R-3.4.2-bioc36/lib
>>-L/usr/local/lib64 -o MACPET.so PeakFinderSubFunctions_SGT_Rcpp.o
>>RcppExports.o -L/home/hpages/R/R-3.4.2-bioc36/lib -lR
>>installing to /home/hpages/R/R-3.4.2-bioc36/library/MACPET/libs
>>** R
>>** inst
>>** byte-compile and prepare package for lazy loading
>>** help
>>...
>>
>>Works for other BioC packages too e.g. InteractionSet
>>(showing compilation

Re: [Bioc-devel] FW: Package build error

2017-10-27 Thread Ioannis Vardaxis 
Hey,

One quick question. When I push again now, do I need to change the version
from 0.99.0 to 0.99.1 or does it change automatically?

Best,
-- 
Ioannis Vardaxis

Stipendiat IMF
NTNU




On 27/10/2017, 19:03, "Hervé Pagès"  wrote:

>Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
>
>hpages@latitude:~/MACPET$ git diff
>diff --git a/DESCRIPTION b/DESCRIPTION
>index d8238b6..061d692 100644
>--- a/DESCRIPTION
>+++ b/DESCRIPTION
>@@ -7,6 +7,7 @@ Author: Ioannis Vardaxis
>  Maintainer: Ioannis Vardaxis 
>  Description: The MACPET package can be used for binding site analysis
>for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM for
>  License: GPL-3
>+SystemRequirements: C++11
>  Encoding: UTF-8
>  LazyData: true
>  ByteCompile: true
>
>
>hpages@latitude:~$ Rbiocdev CMD INSTALL MACPET
>* installing to library '/home/hpages/R/R-3.4.2-bioc36/library'
>* installing *source* package 'MACPET' ...
>** libs
>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>-I/usr/local/include   -fpic  -g -O2 -c
>PeakFinderSubFunctions_SGT_Rcpp.cpp -o PeakFinderSubFunctions_SGT_Rcpp.o
>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>-I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
>g++ -std=gnu++11 -shared -L/home/hpages/R/R-3.4.2-bioc36/lib
>-L/usr/local/lib64 -o MACPET.so PeakFinderSubFunctions_SGT_Rcpp.o
>RcppExports.o -L/home/hpages/R/R-3.4.2-bioc36/lib -lR
>installing to /home/hpages/R/R-3.4.2-bioc36/library/MACPET/libs
>** R
>** inst
>** byte-compile and prepare package for lazy loading
>** help
>...
>
>Works for other BioC packages too e.g. InteractionSet
>(showing compilation output on Mac):
>
> 
>https://bioconductor.org/checkResults/3.6/bioc-LATEST/InteractionSet/verac
>ruz1-install.html
>
>It would be more useful if you showed us the full output of
>'R CMD INSTALL'.
>
>But you should not hesitate to add 'SystemRequirements: C++11', bump
>the version, and see what the single package builder says (provide the
>link if you want to discuss it).
>
>Thanks,
>H.
>
>
>On 10/27/2017 09:50 AM, Ioannis Vardaxis wrote:
>> Hey again,
>>
>>
>> I think I have fixed the \insertRef macro problem now. However I still
>> need help with the c++11 problems I mentioned in the previous email.
>>
>> My package builds and R-checks (and BiocChecks) with no errors and
>>warning
>> though. I get some notes from BiocCheck but I don¹t think they are of
>> immediate importance.
>>
>> Best,
>>
>
>-- 
>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] FW: Package build error

2017-10-27 Thread Ioannis Vardaxis 
Hey,


Ok, I have made the changes to the DESCRIPTION file adding the c++11 you
suggested, and also fixed the Rd files. I will try to push the package
again soon and see what I get.


Thanks,
-- 
Ioannis Vardaxis

Stipendiat IMF
NTNU




On 27/10/2017, 19:03, "Hervé Pagès"  wrote:

>Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
>
>hpages@latitude:~/MACPET$ git diff
>diff --git a/DESCRIPTION b/DESCRIPTION
>index d8238b6..061d692 100644
>--- a/DESCRIPTION
>+++ b/DESCRIPTION
>@@ -7,6 +7,7 @@ Author: Ioannis Vardaxis
>  Maintainer: Ioannis Vardaxis 
>  Description: The MACPET package can be used for binding site analysis
>for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM for
>  License: GPL-3
>+SystemRequirements: C++11
>  Encoding: UTF-8
>  LazyData: true
>  ByteCompile: true
>
>
>hpages@latitude:~$ Rbiocdev CMD INSTALL MACPET
>* installing to library '/home/hpages/R/R-3.4.2-bioc36/library'
>* installing *source* package 'MACPET' ...
>** libs
>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>-I/usr/local/include   -fpic  -g -O2 -c
>PeakFinderSubFunctions_SGT_Rcpp.cpp -o PeakFinderSubFunctions_SGT_Rcpp.o
>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>-I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
>g++ -std=gnu++11 -shared -L/home/hpages/R/R-3.4.2-bioc36/lib
>-L/usr/local/lib64 -o MACPET.so PeakFinderSubFunctions_SGT_Rcpp.o
>RcppExports.o -L/home/hpages/R/R-3.4.2-bioc36/lib -lR
>installing to /home/hpages/R/R-3.4.2-bioc36/library/MACPET/libs
>** R
>** inst
>** byte-compile and prepare package for lazy loading
>** help
>...
>
>Works for other BioC packages too e.g. InteractionSet
>(showing compilation output on Mac):
>
> 
>https://bioconductor.org/checkResults/3.6/bioc-LATEST/InteractionSet/verac
>ruz1-install.html
>
>It would be more useful if you showed us the full output of
>'R CMD INSTALL'.
>
>But you should not hesitate to add 'SystemRequirements: C++11', bump
>the version, and see what the single package builder says (provide the
>link if you want to discuss it).
>
>Thanks,
>H.
>
>
>On 10/27/2017 09:50 AM, Ioannis Vardaxis wrote:
>> Hey again,
>>
>>
>> I think I have fixed the \insertRef macro problem now. However I still
>> need help with the c++11 problems I mentioned in the previous email.
>>
>> My package builds and R-checks (and BiocChecks) with no errors and
>>warning
>> though. I get some notes from BiocCheck but I don¹t think they are of
>> immediate importance.
>>
>> Best,
>>
>
>-- 
>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] Bioc Devel Version issue

2017-10-27 Thread Michael Morgan 
Hi Lori,
It looks like there are additional locations:

> .libPaths()
[1] "/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4" 
"/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library" "/usr/lib/R/library�

I�ve switched to just a single local library path by setting R_LIBS_SITE in my 
.Renviron file.

Thanks for the clue!

Best
Mike

On 27 Oct 2017, at 16:26, Shepherd, Lori 
> wrote:

Are there any other locations where BiocInstaller might already be installed?

.libPaths()


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Bioc-devel 
> on 
behalf of MikeMorgan >
Sent: Friday, October 27, 2017 9:37:54 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Bioc Devel Version issue

Dear Bioc-Developers,

I am trying to switch to Bioc Devel (R version 3.4.2).  There is a
versioning issue with Bioconductor:

 > source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

 > useDevel()
Error: 'devel' version already in use

 > remove.packages("BiocInstaller")
Removing package from �/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4�
(as �lib� is unspecified)
Error in find.package(pkgs, lib) :
   there is no package called �BiocInstaller�

 > source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.2; see
https://bioconductor.org/install/#troubleshoot-biocinstaller

I have followed the instructions in the URL and this does not provide a
solution.  I am attempting to specifically update to use
SingleCellExperiment and the github version of scran.

 > sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2
 >

One of my colleagues currently has the same issue on a Mac with Sierra
10.12.6 running R 3.4.1.

Best wishes

Mike



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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are hereby notified that any disclosure, copying, distribution, or use of this 
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-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



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Re: [Bioc-devel] Accepted packages can't find each other and fail build

2017-10-27 Thread Hervé Pagès 

Hi guys,

On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:

Hi Sokratis,

I added the .BBSoptions file to pcxn when it should have been added to 
pcxnData. The .BBSoptions file should be put in the package that 'Suggests' 
(not 'Depends') on the other. In this case it's pcxnData that needs the 
.BBSoptions. Sorry for the mix up, this has been fixed.

The data package should install with today's builds and be clean on the 
Saturday report. The software package should then install with the Saturday 
builds and be clean on the Sunday report.



This is what should happen:

  - pcxnData should install with today's data-exp builds (they
started this morning) but vignette will still fail (pcxn still
missing)

  - pcxn won't install (will be back to NotNeeded) but should pass
build/check and propagate on Saturday afternoon

  - on Sunday morning, the data exp builds will find pcxn **on line**
(because now it propagated) so will be able to install it so
vignette will finally build and the package will propagate

Thanks for taking care of this,

H.


Valerie


On 10/26/2017 04:26 AM, Shepherd, Lori wrote:

We have already taken care of this on our end and you shouldn't need to do 
anything else.  As always changes reflected may take a few days to reflect in 
the build reports.


The solution is to add a .BBSoptions file with ForceInstall: TRUE to the 
software package.  Since there is a circular dependency this will force install 
the software package even though there will be ERRORs because of the missing 
data package.  On the next build of the data packages, the data package will 
then successfully build finding the software package. Then following, the 
software package will also build finding the data package.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
 on behalf of 
Sokratis Kariotis 
Sent: Thursday, October 26, 2017 4:02:53 AM
To: bioc-devel
Subject: [Bioc-devel] Accepted packages can't find each other and fail build

Hey all,

I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
depends on the data coming from pcxnData. However, in the vignettes of
pcxnData I am using library(pcxn) to demonstrate what can you do with the
data. As a result both packages fail building in BioC 3.6 as they can't
find each other. In a previous pair of packages I am maintaining (pathprint
and pathprintGEOData) I could use the first library in the data package
vignette and building was fine. Is it necessary to remove library(pcxn)
from pcxnData to get them build? Thanks in advance!

Cheers
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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Re: [Bioc-devel] Bioc Devel Version issue

2017-10-27 Thread Shepherd, Lori 
Are there any other locations where BiocInstaller might already be installed?


.libPaths()



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of MikeMorgan 

Sent: Friday, October 27, 2017 9:37:54 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Bioc Devel Version issue

Dear Bioc-Developers,

I am trying to switch to Bioc Devel (R version 3.4.2).  There is a
versioning issue with Bioconductor:

 > source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

 > useDevel()
Error: 'devel' version already in use

 > remove.packages("BiocInstaller")
Removing package from �/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4�
(as �lib� is unspecified)
Error in find.package(pkgs, lib) :
   there is no package called �BiocInstaller�

 > source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.2; see
https://bioconductor.org/install/#troubleshoot-biocinstaller

I have followed the instructions in the URL and this does not provide a
solution.  I am attempting to specifically update to use
SingleCellExperiment and the github version of scran.

 > sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2
 >

One of my colleagues currently has the same issue on a Mac with Sierra
10.12.6 running R 3.4.1.

Best wishes

Mike



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

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Re: [Bioc-devel] "extra" unit tests

2017-10-27 Thread Kasper Daniel Hansen 
I find it really, really hard to write classic unit testing for analytical
/ methods functions.  Unit testing works well and goes a long way for the
part of our stack which is infrastructure and basic classes.  I am
concerned about to what extent our analytic stack actually gets tested
well, even within a package. I am doing some in my packages, but it was
hard and takes execution time.

I agree with Martin that we don't just want to increase the limit on build
time. Most likely that will just mean people spend less time on making
things fast for release. And by "people" I am counting myself.

Best,
Kasper

On Fri, Oct 27, 2017 at 9:49 AM, Sean Davis  wrote:

> We do similar testing (mostly upstream of package building) for GEOmetadb
> and SRAdb. I have been thinking of this problem as "integration testing"
> rather than "unit testing".
>
> https://stackoverflow.com/questions/5357601/whats-the-
> difference-between-unit-tests-and-integration-tests
>
> The build system as it exists is great for unit testing, but not so much
> for integration tests. Workflow-based "testing" might fall under the
> integration testing definition. The unit testing frameworks in R (testthat,
> for example) can be applied to integration testing, but I think it is worth
> keeping the two types of testing somewhat separate for the reasons pointed
> out in the stackoverflow discussion.
>
> Sean
>
>
> On Thu, Oct 26, 2017 at 11:41 PM, Levi Waldron <
> lwaldron.resea...@gmail.com>
> wrote:
>
> > The specific cases I had in mind were curatedMetagenomicData and
> > curatedTCGAData - thinking that the entire databases should be downloaded
> > and syntax-checked at some point, because there could be problems either
> > with the remote data files or how the convenience downloading functions
> > process them. But they're big downloads, so it's slow and hundreds of GB
> > download.
> >
> > Regular http size and timestamp tests would be lightweight and good
> (sounds
> > doable if I don't exactly how yet). But still, in curatedTCGAData
> > especially, the post-download processing is complicated: converting
> tables
> > to SummarizedExperiment and RaggedExperiment, mapping the columns in each
> > omics data type to the clinical & pathological data, and assembling a
> > MultiAssayExperiment containing any combination of omics types for one or
> > more cancer types, and adding metadata (sorry for the shameless plug for
> > the forthcoming curatedTCGAData...). But anyways I'm not sure how to know
> > the objects will be assembled correctly without testing them in normal
> use
> > situations.
> >
> > For non wastefulness, it's actually something where a workflow-type check
> > would make sense - only run if a size, timestamp, or downloader/assembler
> > file is changed, not documentation or some other change unrelated to the
> > download & assembly.
> >
> >
> >
> > On Thu, Oct 26, 2017 at 5:11 AM, Martin Morgan <
> > martin.mor...@roswellpark.org> wrote:
> >
> > > There is currently some capacity in the build system to support
> > 'extended'
> > > builds.
> > >
> > > One possibility would be to provide facilities for packages to 'opt in'
> > to
> > > a distinct 'extended' build, with a (weekly?) build report. One could
> > also
> > > just increase the timeouts of the current builds.
> > >
> > > I think there is considerable value to imposing relatively severe time
> > and
> > > space limitations on packages. A lot of R code is very poorly written,
> > and
> > > the limits force the developer to confront that; admittedly a common
> > > response is not to write better R code. The unit test concept is really
> > > about highly focused tests on modular software; my own 'long' tests
> have
> > in
> > > retrospect often been misguided attempts to throw the kitchen sink at
> > code
> > > and hope that it covers things, rather than to decompose complicated
> > > functions into testable units that can then be assembled with some
> degree
> > > of confidence. Some of the most challenging code to test involves web
> > > services; probably the approach is not to perform numerous queries but
> to
> > > verify that that the service is responsive and providing a version that
> > > your package supports, with non-web queries validating conformance to
> the
> > > version. Often build times are dominated by vignettes analyzing 'real'
> > > data; these are probably more suited to ExperimentData packages where
> > there
> > > are already more liberal space and time limits, and where the extended
> > > computation time does not undermine the pedagogical value of easily
> > > reproduced vignette code.
> > >
> > > I wonder how many people would opt in to an extended build. That
> wasn't,
> > > for instance, what Levi asked about at the start of the thread.
> > >
> > > Martin
> > >
> > >
> > > On 10/25/2017 01:05 PM, Vincent Carey wrote:
> > >
> > >> What about some more hardware to improve throughput?  I think
> > complicating
> > >> the test
> > >>

Re: [Bioc-devel] joining community-bioc slack

2017-10-27 Thread Sean Davis 
Hi, Nate.

Yes, the auto-invite app is not as robust as we would like. I went ahead
and invited you directly.

Sean


On Fri, Oct 27, 2017 at 10:27 AM, Nathan Olson 
wrote:

> Hi, When I recently tried to join the community-bioc slack channel using
> the following link, https://bioc-community.herokuapp.com/, I received a
> `missing_scope` error message. I quick google search indicated the message
> indicates an OAuth error. Does anyone know if someone is working on fixing
> this issue or another way to join the bioc slack channel.
>
> Thanks
> Nate
>
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>
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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] joining community-bioc slack

2017-10-27 Thread Nathan Olson 
Hi, When I recently tried to join the community-bioc slack channel using
the following link, https://bioc-community.herokuapp.com/, I received a
`missing_scope` error message. I quick google search indicated the message
indicates an OAuth error. Does anyone know if someone is working on fixing
this issue or another way to join the bioc slack channel.

Thanks
Nate

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[Bioc-devel] Bioc Devel Version issue

2017-10-27 Thread MikeMorgan 

Dear Bioc-Developers,

I am trying to switch to Bioc Devel (R version 3.4.2).  There is a 
versioning issue with Bioconductor:


> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> useDevel()
Error: 'devel' version already in use

> remove.packages("BiocInstaller")
Removing package from ‘/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Error in find.package(pkgs, lib) :
  there is no package called ‘BiocInstaller’

> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.2; see
https://bioconductor.org/install/#troubleshoot-biocinstaller

I have followed the instructions in the URL and this does not provide a 
solution.  I am attempting to specifically update to use 
SingleCellExperiment and the github version of scran.


> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2
>

One of my colleagues currently has the same issue on a Mac with Sierra 
10.12.6 running R 3.4.1.


Best wishes

Mike



--
The Wellcome Trust Sanger Institute is operated by Genome Research 
Limited, a charity registered in England with number 1021457 and a 
company registered in England with number 2742969, whose registered 
office is 215 Euston Road, London, NW1 2BE.


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Re: [Bioc-devel] Accepted packages can't find each other and fail build

2017-10-27 Thread Obenchain, Valerie 
Hi Sokratis,

I added the .BBSoptions file to pcxn when it should have been added to 
pcxnData. The .BBSoptions file should be put in the package that 'Suggests' 
(not 'Depends') on the other. In this case it's pcxnData that needs the 
.BBSoptions. Sorry for the mix up, this has been fixed.

The data package should install with today's builds and be clean on the 
Saturday report. The software package should then install with the Saturday 
builds and be clean on the Sunday report.

Valerie


On 10/26/2017 04:26 AM, Shepherd, Lori wrote:

We have already taken care of this on our end and you shouldn't need to do 
anything else.  As always changes reflected may take a few days to reflect in 
the build reports.


The solution is to add a .BBSoptions file with ForceInstall: TRUE to the 
software package.  Since there is a circular dependency this will force install 
the software package even though there will be ERRORs because of the missing 
data package.  On the next build of the data packages, the data package will 
then successfully build finding the software package. Then following, the 
software package will also build finding the data package.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
 on 
behalf of Sokratis Kariotis 

Sent: Thursday, October 26, 2017 4:02:53 AM
To: bioc-devel
Subject: [Bioc-devel] Accepted packages can't find each other and fail build

Hey all,

I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
depends on the data coming from pcxnData. However, in the vignettes of
pcxnData I am using library(pcxn) to demonstrate what can you do with the
data. As a result both packages fail building in BioC 3.6 as they can't
find each other. In a previous pair of packages I am maintaining (pathprint
and pathprintGEOData) I could use the first library in the data package
vignette and building was fine. Is it necessary to remove library(pcxn)
from pcxnData to get them build? Thanks in advance!

Cheers
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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Re: [Bioc-devel] issues with access to my Bioconductor repository IntramiRExploreR

2017-10-27 Thread Shepherd, Lori 
Hello,


It looks like when you submitted your package we were still in svn and had 
provided a svn id that was associated with your package. This was the id that 
we would have originally requested in the form for rsa keys.


We have changed the id on our system to match your github id and you should 
have access now.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Surajit 
Bhattacharya 
Sent: Thursday, October 26, 2017 6:11:18 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] issues with access to my Bioconductor repository 
IntramiRExploreR

Hello,


I was trying to make some final changes to my package yesterday (changing the 
README file with the link to the bioconductor page, instead of my github 
repository), but am getting errors in accessing the bioconductor repository.

I followed the flow given in the webpage:


##Added the bioconductor git

$ git remote add upstream 
g...@git.bioconductor.org:packages/IntramiRExploreR.git

##Fetching from upstream

$ git fetch upstream

Permission denied (publickey).

fatal: Could not read from remote repository.



Please make sure you have the correct access rights

and the repository exists.

##Remote -v

$ git remote -v

origin  https://github.com/sbhattacharya3/IntramiRExploreR.git (fetch)

origin  https://github.com/sbhattacharya3/IntramiRExploreR.git (push)

upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git (fetch)

upstreamg...@git.bioconductor.org:packages/IntramiRExploreR.git (push)


I have added my public key to the bioconductor list earlier as told then. Can 
you please guidre me regarding the same.


Thanks,

Surajit



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Re: [Bioc-devel] FW: Package build error

2017-10-27 Thread Hervé Pagès 

Hi Ioannis,

The links to the build results generated  during the submission
process are permanent (or at least remain valid for several months),
so it's easier to provide the link to the particular results:


http://bioconductor.org/spb_reports/MACPET_buildreport_20171026041125.html

As a special bonus, we all get the color version ;-)

R uses its own markup language for man pages, called the Rd format.
\insertRef is not a valid tag in that format. See the "2 Writing R
documentation files" section of the "Writing R Extensions" manual for
more information:


https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-R-documentation-files

Note that "Writing R Extensions" is the primary documentation for R
package developers.

If your code is C++11 and you don't have a src/Makevars or src/Makefile
file, then you need to add

  SystemRequirements: C++11

in the DESCRIPTION file. This will invoke the correct compiler. This
is also explained in "Writing R Extensions" in a subsection dedicated
to "Using C++11 code":


https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-C_002b_002b11-code

Finally, pushing changes to GitHub will automatically start the next
build/check only if you've properly set up the web hook and if you bump
the version of your package, as explained on the Contributions page:

  https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md

Hope this helps,
H.


On 10/26/2017 06:44 PM, Ioannis Vardaxis wrote:


Hey,

Yesterday I submitted an R package to Bioconductor and today I got the build 
results with some error end warnings. Please find the build results attached.

The file is quite long and there are a lot of things there. However when I run 
R-check and BiocCheck on my MAC I don't get any and the package runs fine.

We don't need to go through all the notes in the file, just the first two 
highlighted ones.

For the first one, I get a warning for : unknown macro \insertRef. I have a 
citation file in the package and I can't see any other way to add citation on 
some R functions. Can I change it to something else?

Furthermore, I have only one c++ script, where I use Rcpp package. The header 
of the script is:

#include 
using namespace Rcpp;

I wanted to include functions like std::round, std::log etc, but I got an error 
that round is not in std namespace (see highlight two). How can I tell Rcpp to 
recognise that? Because round Is at std for c++11 I think.
However I don't specify any src/Makevars file, because I though that it is not 
needed anymore.




Finally,

When I make all the changes and fix the errors locally on my mac, I then commit 
and push to GitHub again. Will this automatically start the next build check 
for bioconuctor or do I have to do anything else?


Best
--
Ioannis Vardaxis
Stipendiat IMF
NTNU



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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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