[Bioc-devel] FW: Package build error

Fri Oct 27 20:42:27 CEST 2017

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"
<bioc-devel-bounces at r-project.org on behalf of ioannis.vardaxis at ntnu.no>
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"
><Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>>
>Date: Friday, 27 October 2017 at 19:44
>To: Ioannis Vardaxis
><ioannis.vardaxis at ntnu.no<mailto:ioannis.vardaxis at ntnu.no>>, Hervé Pagès
><hpages at fredhutch.org<mailto:hpages at fredhutch.org>>,
>"bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>"
><bioc-devel at r-project.org<mailto:bioc-devel at 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 
><bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>
>> on behalf of Ioannis Vardaxis
>><ioannis.vardaxis at ntnu.no<mailto:ioannis.vardaxis at ntnu.no>>
>Sent: Friday, October 27, 2017 1:22:26 PM
>To: Hervé Pagès; bioc-devel at r-project.org<mailto:bioc-devel at 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"
><hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
>
>>Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
>>
>>hpages at 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
>><ioannis.vardaxis at ntnu.no<mailto:ioannis.vardaxis at ntnu.no>>
>>  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 at 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/vera
>>c
>>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 donÂ¹t 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: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
>>Phone:  (206) 667-5791
>>Fax:    (206) 667-1319
>
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