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 <Rcpp.h> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: [History]Bioconductor Single Package Builder.pdf Type: application/pdf Size: 253195 bytes Desc: [History]Bioconductor Single Package Builder.pdf URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20171027/fbb84790/attachment.pdf>
[Bioc-devel] FW: Package build error
11 messages · Ioannis Vardaxis, Shepherd, Lori, 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 <Rcpp.h> 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
_______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=SaEymTCrfYWhmSxfpclcj4f8BhbErU5AN8I0Nq8hJW8&s=ig52drgXtWvHklhJXwxOARxox3Q-LFHsXWUqukG45Ak&e=
Herv? Pag?s 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 Phone: (206) 667-5791 Fax: (206) 667-1319
Hey,
Thanks for the answer. Sorry for not including the link!
For the references part: I am using roxygen2 to create the Rd formats and
the \insertRef{link to bib reference file} should work for that. It looked
like:
#' @references \insertRef{macpetcite}{MACPET}
However I followed your suggestion and used the \references{} macro from
writing R documentation files, then the reference looks like:
#'@references
#' \references{
#' Consortium EP (2012) \emph{An integrated encyclopedia of DNA elements
in the human genome.}.
#' Nature, 489(7414), pp. 57?74.
\url{http://dx.doi.org/10.1038/nature11247}.
#' }
When I build the package I get get a warning for that: "unexpected section
header '\references??, the reference is there however when I search for
the documentation in R, but this warning is new.
Moreover, for the C++11: I have my cpp script which is mainly written
using Rcpp so the headers are:
#include <Rcpp.h>
using namespace Rcpp;
I included the SystemRequirements: C++11 in the DESCRIPTION file. But when
I look into the script I get error symbols on the left side for example:
For "std::ceil? I get the ?call to ceil is ambiguous? however I specify
std:: so the error should not be there right? (same error for std::log,
std::round, std::sqrt, std::exp)
Moreover: for ?INFINITY? I get ?used of undeclared identifier INFINITY?,
but INFINITY is in c++11, so this should not be there either.
Furthermore, for "std::isnan? I get ?no member named isnan in namespace
std?, but it should be in c++11.
However when I go to http://en.cppreference.com/w/cpp/numeric/math/exp and
check the function there, it says that the header for the above mentioned
functions is <cmath>
So I wonder if I should include something else in the headers of the
script:
#include <cmath> for example, although I did that and the errors are
there.
The package builds and runs, but I?m sure I am gonna get errors again
when I submit it.
Best,
Ioannis Vardaxis Stipendiat IMF NTNU On 27/10/2017, 08:01, "Herv? Pag?s" <hpages at fredhutch.org> wrote: >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-doc >umentation-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 <Rcpp.h> >> 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 >> >> >> >> _______________________________________________ >> Bioc-devel at r-project.org mailing list >> >>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman >>_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd >>GbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=SaEymTCrfYWhmSxfpclcj4f8BhbErU5AN8I0Nq8hJ >>W8&s=ig52drgXtWvHklhJXwxOARxox3Q-LFHsXWUqukG45Ak&e= >> > >-- >Herv? Pag?s > >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 >Phone: (206) 667-5791 >Fax: (206) 667-1319
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 don?t think they are of immediate importance. Best,
Ioannis Vardaxis Stipendiat IMF NTNU On 27/10/2017, 08:01, "Herv? Pag?s" <hpages at fredhutch.org> wrote: >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-doc >umentation-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 <Rcpp.h> >> 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 >> >> >> >> _______________________________________________ >> Bioc-devel at r-project.org mailing list >> >>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman >>_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd >>GbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=SaEymTCrfYWhmSxfpclcj4f8BhbErU5AN8I0Nq8hJ >>W8&s=ig52drgXtWvHklhJXwxOARxox3Q-LFHsXWUqukG45Ak&e= >> > >-- >Herv? Pag?s > >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 >Phone: (206) 667-5791 >Fax: (206) 667-1319
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> 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/veracruz1-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 don??t think they are of immediate importance. Best,
Herv? Pag?s 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 Phone: (206) 667-5791 Fax: (206) 667-1319
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, "Herv? Pag?s" <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> > 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 don??t think they are of >> immediate importance. >> >> Best, >> > >-- >Herv? Pag?s > >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 >Phone: (206) 667-5791 >Fax: (206) 667-1319
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, "Herv? Pag?s" <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> > 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 don??t think they are of >> immediate importance. >> >> Best, >> > >-- >Herv? Pag?s > >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 >Phone: (206) 667-5791 >Fax: (206) 667-1319
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> on behalf of Ioannis Vardaxis <ioannis.vardaxis at ntnu.no>
Sent: Friday, October 27, 2017 1:22:26 PM
To: Herv? Pag?s; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] FW: Package build error
Sent: Friday, October 27, 2017 1:22:26 PM
To: Herv? Pag?s; 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, "Herv? Pag?s" <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> > 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 don??t think they are of >> immediate importance. >> >> Best, >> > >-- >Herv? Pag?s > >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 >Phone: (206) 667-5791 >Fax: (206) 667-1319 _______________________________________________ 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.
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 ? in the Rd files. I just write ? 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>>, Herv? Pag?s <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: Herv? Pag?s; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] FW: Package build error
Sent: Friday, October 27, 2017 1:22:26 PM
To: Herv? Pag?s; 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, "Herv? Pag?s" <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 don??t think they are of >> immediate importance. >> >> Best, >> > >-- >Herv? Pag?s > >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.
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 ? in the Rd files. >I just write ? 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>>, Herv? Pag?s ><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: Herv? Pag?s; 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, "Herv? Pag?s" ><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 don??t think they are of >>> immediate importance. >>> >>> Best, >>> >> >>-- >>Herv? Pag?s >> >>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]] > >_______________________________________________ >Bioc-devel at r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/bioc-devel
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,
Herv? Pag?s 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 Phone: (206) 667-5791 Fax: (206) 667-1319