[Bioc-devel] Fwd: OmicsMarkeR problems reported by the "Build/check report" for BioC 3.1
I apologize if this is the incorrect place to post this but I need some assistance with the following build report. I submitted my fix for this problem two days ago to my git repo which has the corresponding svn bridge. Everything builds correctly on my system and Travis CI but doesn't appear to do so for bioconductor's servers. I tried to access my svn to check if my updates were mirrored from my git repo at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR but after logging in all I get is an 'Internal Server Error'. I want to address this problem but I don't know how to proceed at this point. Regards, Charles -- Forwarded message -- From: Date: Tue, Jul 21, 2015 at 1:12 PM Subject: OmicsMarkeR problems reported by the "Build/check report" for BioC 3.1 To: cdeterma...@gmail.com [This is an automatically generated email. Please don't reply.] Hi OmicsMarkeR maintainer, According to the "Build/check report" for BioC 3.1, the OmicsMarkeR package has the following problem(s): o ERROR for 'R CMD build' on zin2. See the details here: http://bioconductor.org/checkResults/3.1/bioc-LATEST/OmicsMarkeR/zin2-buildsrc.html Please take the time to address this then use your Subversion account when you are ready to commit a fix to your package. Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: http://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: http://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Fwd: OmicsMarkeR problems reported by the "Build/check report" for BioC 3.1
I can get in with 'readonly' but not my user account. Is there any way for me to reset it? Charles On Tue, Jul 21, 2015 at 1:44 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Charles Determan" > > To: bioc-devel@r-project.org > > Sent: Tuesday, July 21, 2015 11:23:00 AM > > Subject: [Bioc-devel] Fwd: OmicsMarkeR problems reported by the > "Build/check report" for BioC 3.1 > > > > I apologize if this is the incorrect place to post this but I need > > some > > assistance with the following build report. I submitted my fix for > > this > > problem two days ago to my git repo which has the corresponding svn > > bridge. Everything builds correctly on my system and Travis CI but > > doesn't > > appear to do so for bioconductor's servers. I tried to access my svn > > to > > check if my updates were mirrored from my git repo at > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR > > but > > after logging in all I get is an 'Internal Server Error'. > > > > I can't reproduce this; if I paste that url into a web browser and log in > either with my svn > username and password or readonly/readonly, I don't get an error. > > > I want to address this problem but I don't know how to proceed at > > this > > point. > > > The error you were emailed about was in release. The problem here is that > something in the CRAN package assertive has changed. It looks like you have > not modified release at all. > > The error in devel is different: > > > http://www.bioconductor.org/checkResults/devel/bioc-LATEST/OmicsMarkeR/zin1-checksrc.html > > Not sure if this is related to the assertive package or if it's something > introduced in your commit. As I recall, before this commit, both release > and devel had the same error that we are now seeing in release. > > FYI, to make changes to release, you need to check out > > > https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/OmicsMarkeR > > Dan > > > > > > > Regards, > > Charles > > > > > > -- Forwarded message -- > > From: > > Date: Tue, Jul 21, 2015 at 1:12 PM > > Subject: OmicsMarkeR problems reported by the "Build/check report" > > for BioC > > 3.1 > > To: cdeterma...@gmail.com > > > > > > [This is an automatically generated email. Please don't reply.] > > > > Hi OmicsMarkeR maintainer, > > > > According to the "Build/check report" for BioC 3.1, > > the OmicsMarkeR package has the following problem(s): > > > > o ERROR for 'R CMD build' on zin2. See the details here: > > > > > http://bioconductor.org/checkResults/3.1/bioc-LATEST/OmicsMarkeR/zin2-buildsrc.html > > > > Please take the time to address this then use your Subversion account > > when you are ready to commit a fix to your package. > > > > Notes: > > > > * This was the status of your package at the time this email was > > sent to > > you. > > Given that the online report is updated daily (in normal > > conditions) you > > could see something different when you visit the URL(s) above, > > especially if > > you do so several days after you received this email. > > > > * It is possible that the problems reported in this report are > > false > > positives, > > either because another package (from CRAN or Bioconductor) breaks > > your > > package (if yours depends on it) or because of a Build System > > problem. > > If this is the case, then you can ignore this email. > > > > * Please check the report again 24h after you've committed your > > changes > > to the > > package and make sure that all the problems have gone. > > > > * If you have questions about this report or need help with the > > maintenance of your package, please use the Bioc-devel mailing > > list: > > > > http://bioconductor.org/help/mailing-list/ > > > > (all package maintainers are requested to subscribe to this list) > > > > For immediate notification of package build status, please > > subscribe to your package's RSS feed. Information is at: > > > > http://bioconductor.org/developers/rss-feeds/ > > > > Thanks for contributing to the Bioconductor project! > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Fwd: OmicsMarkeR problems reported by the "Build/check report" for BioC 3.1
Okay, I made it in and committed the bug fix (svn commit). The package should build properly now. Thank you for your help. Charles On Tue, Jul 21, 2015 at 1:58 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Charles Determan" > > To: "Dan Tenenbaum" > > Cc: bioc-devel@r-project.org > > Sent: Tuesday, July 21, 2015 11:52:49 AM > > Subject: Re: [Bioc-devel] Fwd: OmicsMarkeR problems reported by the > "Build/check report" for BioC 3.1 > > > > > > > > I can get in with 'readonly' but not my user account. Is there any > > way for me to reset it? > > See > http://www.bioconductor.org/developers/how-to/git-mirrors/#i-dont-know-my-subversion-username-andor-password-what-do-i-do > > Dan > > > > > > > Charles > > > > > > > > On Tue, Jul 21, 2015 at 1:44 PM, Dan Tenenbaum < > > dtene...@fredhutch.org > wrote: > > > > > > > > > > - Original Message - > > > From: "Charles Determan" < cdeterma...@gmail.com > > > > To: bioc-devel@r-project.org > > > Sent: Tuesday, July 21, 2015 11:23:00 AM > > > Subject: [Bioc-devel] Fwd: OmicsMarkeR problems reported by the > > > "Build/check report" for BioC 3.1 > > > > > > I apologize if this is the incorrect place to post this but I need > > > some > > > assistance with the following build report. I submitted my fix for > > > this > > > problem two days ago to my git repo which has the corresponding svn > > > bridge. Everything builds correctly on my system and Travis CI but > > > doesn't > > > appear to do so for bioconductor's servers. I tried to access my > > > svn > > > to > > > check if my updates were mirrored from my git repo at > > > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR > > > but > > > after logging in all I get is an 'Internal Server Error'. > > > > > > > I can't reproduce this; if I paste that url into a web browser and > > log in either with my svn > > username and password or readonly/readonly, I don't get an error. > > > > > I want to address this problem but I don't know how to proceed at > > > this > > > point. > > > > > > The error you were emailed about was in release. The problem here is > > that something in the CRAN package assertive has changed. It looks > > like you have not modified release at all. > > > > The error in devel is different: > > > > > http://www.bioconductor.org/checkResults/devel/bioc-LATEST/OmicsMarkeR/zin1-checksrc.html > > > > Not sure if this is related to the assertive package or if it's > > something introduced in your commit. As I recall, before this > > commit, both release and devel had the same error that we are now > > seeing in release. > > > > FYI, to make changes to release, you need to check out > > > > > https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/OmicsMarkeR > > > > Dan > > > > > > > > > > > > Regards, > > > Charles > > > > > > > > > -- Forwarded message -- > > > From: < bbs-nore...@bioconductor.org > > > > Date: Tue, Jul 21, 2015 at 1:12 PM > > > Subject: OmicsMarkeR problems reported by the "Build/check report" > > > for BioC > > > 3.1 > > > To: cdeterma...@gmail.com > > > > > > > > > [This is an automatically generated email. Please don't reply.] > > > > > > Hi OmicsMarkeR maintainer, > > > > > > According to the "Build/check report" for BioC 3.1, > > > the OmicsMarkeR package has the following problem(s): > > > > > > o ERROR for 'R CMD build' on zin2. See the details here: > > > > > > > http://bioconductor.org/checkResults/3.1/bioc-LATEST/OmicsMarkeR/zin2-buildsrc.html > > > > > > > > > > Please take the time to address this then use your Subversion > > > account > > > when you are ready to commit a fix to your package. > > > > > > Notes: > > > > > > * This was the status of your package at the time this email was > > > sent to > > > you. > > > Given that the online report is updated daily (in normal > > > conditions) you > > > could see something different whe
Re: [Bioc-devel] using covr with the parallel package
This may be more appropriate to ask the covr package maintainer on his github page (https://github.com/jimhester/covr/issues). Charles On Mon, Aug 17, 2015 at 1:13 PM, Leonard Goldstein < goldstein.leon...@gene.com> wrote: > Hi Jim, > > I noticed that when covr calculates test coverage, functions called > inside mclapply or mcmapply with argument mc.preschedule = FALSE are > considered untested (even if unit tests exist) > > When running checks I only use one core. So an easy fix would be to > set mc.preschedule to TRUE if mc.cores = 1. But I was wondering if you > are aware of this behavior and whether there is a way to avoid it? > > Many thanks for your help. > > Leonard > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor Build Still Failing on Travis CI
This initially came to my attention with this question on StackOverflow ( http://stackoverflow.com/questions/32139378/travis-ci-failing-to-install-bioconductor?noredirect=1#comment52184421_32139378). I have noticed that my own bioconductor package has continued to fail over the past several days when it is trying to install bioconductor dependencies. I am able to install bioconductor packages locally but the Travis environment continues to fail. I want to check here to find out if there is still something going on with bioconductor or if this is a travis ci issue? Note, my package built successfully previously and I have made no changes to my .travis.yml file. Regards, Charles [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Trouble installing S4Vectors?
I am trying to run the basic install with biocLite. I am running R 3.2.2
on Ubuntu 14.04.
I install the BiocInstaller package with
source("http://bioconductor.org/biocLite.R";)
I then try again to just install S4Vectors but it errors out on the
src_utils file with the following error:
str_utils.c: In function ‘get_svn_time’:
str_utils.c:259:2: warning: implicit declaration of function ‘tzset’
[-Wimplicit-function-declaration]
tzset();
^
str_utils.c:261:18: error: ‘timezone’ undeclared (first use in this
function)
utc_offset = - (timezone / 3600);
^
str_utils.c:261:18: note: each undeclared identifier is reported only once
for each function it appears in
make: *** [str_utils.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’
Did I miss something?
Thanks,
Charles
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Trouble installing S4Vectors?
I am simply using gcc-4.8
Here is the full output:
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘S4Vectors’
trying URL '
http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.6.3.tar.gz
'
Content type 'application/x-gzip' length 187491 bytes (183 KB)
==
downloaded 183 KB
* installing *source* package ‘S4Vectors’ ...
** libs
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c AEbufs.c -o AEbufs.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c DataFrame_class.c -o DataFrame_class.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c Hits_class.c -o Hits_class.o
Hits_class.c: In function ‘Hits_new’:
Hits_class.c:157:13: warning: ‘q_hits2’ may be used uninitialized in this
function [-Wmaybe-uninitialized]
tsort_hits(q_hits2, s_hits, qh_out, sh_out, nhit,
^
Hits_class.c:144:7: note: ‘q_hits2’ was declared here
int *q_hits2, *qh_out, *sh_out;
^
Hits_class.c:233:14: warning: ‘revmap’ may be used uninitialized in this
function [-Wmaybe-uninitialized]
defineVar(install(translateChar(symbol)), revmap, revmap_envir);
^
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c List_class.c -o List_class.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c Rle_class.c -o Rle_class.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c Rle_utils.c -o Rle_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c SEXP_utils.c -o SEXP_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c SimpleList_class.c -o SimpleList_class.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c anyMissing.c -o anyMissing.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c eval_utils.c -o eval_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c hash_utils.c -o hash_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c int_utils.c -o int_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c logical_utils.c -o logical_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c safe_arithm.c -o safe_arithm.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c sort_utils.c -o sort_utils.o
ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3
-std=c99 -c str_utils.c -o str_utils.o
str_utils.c: In function ‘get_svn_time’:
str_utils.c:259:2: warning: implicit declaration of function ‘tzset’
[-Wimplicit-function-declaration]
tzset();
^
str_utils.c:261:18: error: ‘timezone’ undeclared (first use in this
function)
utc_offset = - (timezone / 3600);
^
str_utils.c:261:18: note: each undeclared identifier is reported only once
for each function it appears in
make: *** [str_utils.o] Error 1
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/home/cdeterman/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors’
On Thu, Aug 27, 2015 at 12:04 PM, Hervé Pagès wrote:
> Hi Charles,
>
> What compiler do you use? Please show the entire output of
> biocLite("S4Vectors") plus your sessionInfo(). Thanks!
>
> H.
>
>
> On 08/27/2015 06:19 AM, Charles Determan wrote:
>
>> I am trying to run the basic install with biocLite. I am running R 3.2.2
>> on Ubuntu 14.04.
>>
>> I install the BiocInstaller package with
>>
>> source("http://bioconductor.org/biocLite.R";)
>>
>> I then try again to just install S4Vectors but it errors out on the
>> src_utils file with the following error:
>>
>> str_utils.c: In function ‘get_svn_time’:
>> str_utils.c:259:2: warning: implicit declaration of function ‘tzset’
>> [-Wimplicit-function-declaration]
>>tzset();
>>^
>> str_utils.c:261:18: error: ‘timezone’ undeclared (first use in this
>> function)
>>utc_offset = - (timezone / 3600);
>>^
>> str_utils.c:261:18: note: each undeclared identifier is reported only once
>> for each function it appears in
>> make: *** [str_utils.o] Error 1
>> ERROR: compilation failed for package ‘S4Vectors’
>>
>> Did I miss something?
>>
>> Thanks,
>> Charles
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>>
Re: [Bioc-devel] Trouble installing S4Vectors?
Thanks Herve, that solved the problem. It installed correctly now. Regards, Charles On Thu, Aug 27, 2015 at 4:14 PM, Hervé Pagès wrote: > On 08/27/2015 10:21 AM, Charles Determan wrote: > >> I am simply using gcc-4.8 >> >> Here is the full output: >> >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2. >> Installing package(s) ‘S4Vectors’ >> trying URL >> ' >> http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.6.3.tar.gz >> ' >> Content type 'application/x-gzip' length 187491 bytes (183 KB) >> == >> downloaded 183 KB >> >> * installing *source* package ‘S4Vectors’ ... >> ** libs >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c AEbufs.c -o AEbufs.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c DataFrame_class.c -o DataFrame_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c Hits_class.c -o Hits_class.o >> Hits_class.c: In function ‘Hits_new’: >> Hits_class.c:157:13: warning: ‘q_hits2’ may be used uninitialized in >> this function [-Wmaybe-uninitialized] >> tsort_hits(q_hits2, s_hits, qh_out, sh_out, nhit, >> ^ >> Hits_class.c:144:7: note: ‘q_hits2’ was declared here >>int *q_hits2, *qh_out, *sh_out; >> ^ >> Hits_class.c:233:14: warning: ‘revmap’ may be used uninitialized in this >> function [-Wmaybe-uninitialized] >>defineVar(install(translateChar(symbol)), revmap, revmap_envir); >>^ >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c List_class.c -o List_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c R_init_S4Vectors.c -o R_init_S4Vectors.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c Rle_class.c -o Rle_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c Rle_utils.c -o Rle_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c SEXP_utils.c -o SEXP_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c SimpleList_class.c -o SimpleList_class.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c anyMissing.c -o anyMissing.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c eval_utils.c -o eval_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c hash_utils.c -o hash_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c int_utils.c -o int_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c logical_utils.c -o logical_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c safe_arithm.c -o safe_arithm.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c sort_utils.c -o sort_utils.o >> ccache gcc-4.8 -I/usr/share/R/include -DNDEBUG -fpic -Wall -O3 >> -std=c99 -c str_utils.c -o str_utils.o >> str_utils.c: In function ‘get_svn_time’: >> str_utils.c:259:2: warning: implicit declaration of function ‘tzset’ >> [-Wimplicit-function-declaration] >>tzset(); >>^ >> str_utils.c:261:18: error: ‘timezone’ undeclared (first use in this >> function) >>utc_offset = - (timezone / 3600); >>^ >> str_utils.c:261:18: note: each undeclared identifier is reported only >> once for each function it appears in >> make: *** [str_utils.o] Error 1 >> ERROR: compilation failed for package ‘S4Vectors’ >> * removing ‘/home/cdeterman/R/x86_64-pc-linux-gnu-library/3.2/S4Vectors’ >> > > The -std=c99 compilation flag seems to be causing this. On our build > machines that use gcc (i.e. Linux, Windows, and Snow Leopard), we use > -std=gnu99. Check what flag your R is using by running: > > R CMD config CC > > in your terminal. My understanding is that gcc doesn't fully support > c99 yet, and that R packages are only required to support gnu99. > AFAIK the standard procedure for configuring/compiling/installing > R should set this to gnu99 when gcc is the default compiler. > So I'm not not sure why R is configured to use -std=c99 on your > system. > > Any
Re: [Bioc-devel] C library or C package API for regular expressions
Hi Jiri, I believe you can use the BH package. It contains most of the Boost headers. Regards, Charles On Saturday, January 23, 2016, Jiří Hon wrote: > Dear package developers, > > I would like to ask you for advice. Please, what is the most seamless > way to use regular expressions in C/C++ code of R/Bioconductor package? > Is it allowed to bundle some C/C++ library for that (like PCRE or > Boost.Regex)? Or is there existing C API of some package I can depend on > and import? > > Thank you a lot for your attention and please have a nice day :) > > Jiri Hon > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Updating package
Hi, I received a notification that my package was failing some tests. I have since made the necessary fixes and pushed my changes to the github repo. Previously this would result in http://gitsvn.bioconductor.org/git-push-hook updating the package for bioconductor. I noticed however that this delivery fails and that the git-svn bridge is no longer available. How should I modify my current repository to update my package accordingly? I have my local changes in the 'devel' branch. I ran the update_ remotes.sh I run 'git svn rebase' but I get the following error: Can't create session: Unable to connect to a repository at URL ' https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR': Unexpected server error 500 'Internal Server Error' on '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at /mingw64/share/perl5/site_perl/Git/SVN.pm line 717. What did I miss here? Thanks, Charles [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Updating package
Not to be pushy but did anyone have any insights with this? I would hate to have my package still sitting with the bug fix it requires. Thanks, Charles On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan wrote: > Hi, > > I received a notification that my package was failing some tests. I have > since made the necessary fixes and pushed my changes to the github repo. > Previously this would result in http://gitsvn.bioconductor. > org/git-push-hook updating the package for bioconductor. I noticed > however that this delivery fails and that the git-svn bridge is no longer > available. > > How should I modify my current repository to update my package > accordingly? > > I have my local changes in the 'devel' branch. > I ran the update_ remotes.sh > I run 'git svn rebase' but I get the following error: > > Can't create session: Unable to connect to a repository at URL ' > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR': > Unexpected server error 500 'Internal Server Error' on > '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at > /mingw64/share/perl5/site_perl/Git/SVN.pm line 717. > > What did I miss here? > Thanks, > > Charles > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Updating package
That seems to have been the issue. It had been some time since I needed to commit to bioconductor I forgot my username was different. Thank you Martin for pointing that simple problem out. I have now 'dcommit' my 'devel' branch so if I understand correctly the changes should be with bioconductor to apply accordingly. Regards, Charles On Thu, Jan 5, 2017 at 9:22 AM, Martin Morgan wrote: > On 01/05/2017 10:18 AM, Charles Determan wrote: > >> Not to be pushy but did anyone have any insights with this? I would hate >> to have my package still sitting with the bug fix it requires. >> > > maybe svn credentials, > > git svn rebase --username=c.determan > > ?? > > >> Thanks, >> Charles >> >> On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan >> wrote: >> >> Hi, >>> >>> I received a notification that my package was failing some tests. I have >>> since made the necessary fixes and pushed my changes to the github repo. >>> Previously this would result in http://gitsvn.bioconductor. >>> org/git-push-hook updating the package for bioconductor. I noticed >>> however that this delivery fails and that the git-svn bridge is no longer >>> available. >>> >>> How should I modify my current repository to update my package >>> accordingly? >>> >>> I have my local changes in the 'devel' branch. >>> I ran the update_ remotes.sh >>> I run 'git svn rebase' but I get the following error: >>> >>> Can't create session: Unable to connect to a repository at URL ' >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR >>> ': >>> Unexpected server error 500 'Internal Server Error' on >>> '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at >>> /mingw64/share/perl5/site_perl/Git/SVN.pm line 717. >>> >>> What did I miss here? >>> Thanks, >>> >>> Charles >>> >>> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Updating package
I committed my changes earlier this morning from the 'devel' branch via the 'git svn dcommit --add-author-from' the website ( https://www.bioconductor.org/developers/how-to/git-mirrors/). I have yet to see any changes on the build page though for the `devel` ( http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/). Did I miss another step or is the build process reporting slow or perhaps I am looking in the wrong place still? Regards, Charles On Thu, Jan 5, 2017 at 9:47 AM, Charles Determan wrote: > That seems to have been the issue. It had been some time since I needed > to commit to bioconductor I forgot my username was different. Thank you > Martin for pointing that simple problem out. I have now 'dcommit' my > 'devel' branch so if I understand correctly the changes should be with > bioconductor to apply accordingly. > > Regards, > Charles > > On Thu, Jan 5, 2017 at 9:22 AM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >> On 01/05/2017 10:18 AM, Charles Determan wrote: >> >>> Not to be pushy but did anyone have any insights with this? I would hate >>> to have my package still sitting with the bug fix it requires. >>> >> >> maybe svn credentials, >> >> git svn rebase --username=c.determan >> >> ?? >> >> >>> Thanks, >>> Charles >>> >>> On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan >> > >>> wrote: >>> >>> Hi, >>>> >>>> I received a notification that my package was failing some tests. I >>>> have >>>> since made the necessary fixes and pushed my changes to the github repo. >>>> Previously this would result in http://gitsvn.bioconductor. >>>> org/git-push-hook updating the package for bioconductor. I noticed >>>> however that this delivery fails and that the git-svn bridge is no >>>> longer >>>> available. >>>> >>>> How should I modify my current repository to update my package >>>> accordingly? >>>> >>>> I have my local changes in the 'devel' branch. >>>> I ran the update_ remotes.sh >>>> I run 'git svn rebase' but I get the following error: >>>> >>>> Can't create session: Unable to connect to a repository at URL ' >>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR >>>> ': >>>> Unexpected server error 500 'Internal Server Error' on >>>> '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at >>>> /mingw64/share/perl5/site_perl/Git/SVN.pm line 717. >>>> >>>> What did I miss here? >>>> Thanks, >>>> >>>> Charles >>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> Bioc-devel@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocCheck Error 'duplicate label install'?
Greetings, Apologies if this is a double post, I was over zealous in my initial submission that I didn't wait for my membership to be confirmed. I have 'finished' creating a package I would like to submit to bioconductor. As per the instructions on the bioconductor website I am trying to get the package to pass the BiocCheck function but I keep getting the following error: Error in parse_block(g[-1], g[1], params.src) : duplicate label 'install' The package also passes through R CMD Check with no errors or warnings. If someone could kindly explain what this error means I would sincerely appreciate it. Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Submitting a new package
I have finished a new package recently that I would like to submit to bioconductor. I have read through the package guidelines and I believe I understand the package submission process but embarrassingly I cannot figure out how to actually submit the package? Could someone kindly explain where I actually submit the package for review? Regards, -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitting a new package
Thanks Dan, could you confirm that the email statement (packages NEAR bioconductor POINT org) means packa...@bioconductor.org ? I don't recognize the NEAR notation. Charles On Fri, Mar 13, 2015 at 1:59 PM, Dan Tenenbaum wrote: > > > - Original Message ----- > > From: "Charles Determan Jr" > > To: Bioc-devel@r-project.org > > Sent: Friday, March 13, 2015 11:57:24 AM > > Subject: [Bioc-devel] Submitting a new package > > > > I have finished a new package recently that I would like to submit to > > bioconductor. I have read through the package guidelines and I > > believe I > > understand the package submission process but embarrassingly I cannot > > figure out how to actually submit the package? Could someone kindly > > explain where I actually submit the package for review? > > > > See the very bottom of > http://bioconductor.org/developers/package-submission/ > > Dan > > > > > > Regards, > > > > -- > > Dr. Charles Determan, PhD > > Integrated Biosciences > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
