[Bioc-devel] FW: Package build error

Ioannis Vardaxis ioannis.vardaxis at ntnu.no
Fri Oct 27 20:08:03 CEST 2017


Here is the report:


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
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.

Ioannis Vardaxis
Stipendiat IMF

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


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


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?

Ioannis Vardaxis

Stipendiat IMF

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
>index d8238b6..061d692 100644
>@@ -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/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/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):
>It would be more useful if you showed us the full output of
>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).
>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
>> 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: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319

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