[Bioc-devel] FW: Package build error

Fri Oct 27 20:08:03 CEST 2017

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/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 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

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://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]]