Re: [Bioc-devel] problem installing biocLite package
On Tue, Jun 25, 2013 at 9:12 AM, Marinus Pennings wrote:
> Hello,
>
> I initially sent this email to the regular bioconductor mailing list
> but they told me I probably should sent it here.
>
Actually, what was suggested was to come up with a minimal test case
and email the R-devel list
(http://stat.ethz.ch/mailman/listinfo/r-devel), not the bioc-devel
list. Please see this email:
https://stat.ethz.ch/pipermail/bioconductor/2013-June/053192.html
But be sure you come up with the minimal test case first. If you just
email R-devel asking about an edgeR install problem, they will not
help you.
Thanks,
Dan
> I'm installing some bioclite packages for one of our users. Config
> params are
>
> R version: 3.0.1
> build with: intel composerxe version 13 using mkl
>
> I installed using the info on the website. The first two steps are
> executed without error
> |
> source("http://bioconductor.org/biocLite.R";)
> biocLite()|
>
> However, when I try to execute the command
>
> biocLite('edgeR')
>
>
> I get the error messages below.
>
> NOTE, when I used a gnu non-mkl version of R 3.0.1 I was able to install
> everything without any problem:
>
> output of "biocLite('edgeR')":
>
> > biocLite('edgeR')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
> Installing package(s) 'edgeR'
>
>
> trying URL
> 'http://bioconductor.org/packages/2.12/bioc/src/contrib/edgeR_3.2.3.tar.gz'
> Content type 'application/x-gzip' length 1211896 bytes (1.2 Mb)
> opened URL
>
> ==
> downloaded 1.2 Mb
>
> * installing *source* package 'edgeR' ...
> ** libs
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_exact_test_by_deviance.cpp -o
> R_exact_test_by_deviance.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_loess_by_col.cpp -o R_loess_by_col.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_cr_adjust.cpp -o R_cr_adjust.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_levenberg.cpp -o R_levenberg.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_one_group.cpp -o R_one_group.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c R_simple_good_turing.cpp -o R_simple_good_turing.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c core/adj_coxreid.cpp -o core/adj_coxreid.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c core/glm_levenberg.cpp -o core/glm_levenberg.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c core/glm_one_group.cpp -o core/glm_one_group.o
> icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
> -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
> -fp-model precise -c core/interpolator.cpp -o core/interpolator.o
> icc -std=gnu99 -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include
> -DNDEBUG -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3
> -g -fp-model precise -c core/fmm_spline.c -o core/fmm_spline.o
> icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o
> R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o
> R_one_group.o R_simple_good_turing.o core/adj_coxreid.o
> core/glm_levenberg.o core/glm_one_group.o core/interpolator.o
> core/fmm_spline.o -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64
> -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport
> -lifcoremt -limf -lsvml -lm -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
> /g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/libimf.so:
> warning: warning: feupdateenv is not implemented and will always fail
> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In
> function `_start':
> (.text+0x20): undefined reference to `main'
> R_exact_test_by_deviance.o: In function `R_exact_test_by_deviance':
> /scratch/pennings/tmp/Rtmp8dpzIj/R.IN
Re: [Bioc-devel] AnnotationHubServer requires AnnotationHubData of a particular vintage
On Tue, Jun 25, 2013 at 9:30 AM, Tim Triche, Jr. wrote:
> I've been having this problem for a while with the package:
>
> tim@tim-ThinkPad-T420s:~/bioc-devel$ more
> /home/tim/bioc-devel/AnnotationHubServer.Rcheck/00install.out
> * installing *source* package ‘AnnotationHubServer’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in match.fun(FUN) : node stack overflow
> ERROR: lazy loading failed for package ‘AnnotationHubServer’
> * removing
> ‘/home/tim/bioc-devel/AnnotationHubServer.Rcheck/AnnotationHubServer’
>
> This morning it dawned on me that perhaps installing AnnotationHubData was
> a prerequisite, so I gave it a shot:
>
> [1] Creating log directory /home/tim/.AnnotationHubData
> * DONE (AnnotationHubData)
> tim@tim-ThinkPad-T420s:~/bioc-devel$ R CMD INSTALL AnnotationHubServer/*
> installing to library ‘/usr/lib64/R/library’
> * installing *source* package ‘AnnotationHubServer’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> rmongodb package (mongo-r-driver) loaded
> Use 'help("mongo")' to get started.
>
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> rmongodb package (mongo-r-driver) loaded
> Use 'help("mongo")' to get started.
>
> * DONE (AnnotationHubServer)
>
>
> So perhaps that should go in the DESCRIPTION file for the latter, along
> with a revision number? It would seem that I must have had
> AnnotationHubData from an older vintage installed, but said older vintage
> was not satisfactory, thus, error.
>
> Anyways. Just in case anyone else has the same issue, here it is.
>
Thanks, I've committed the following change to devel:
svn diff
Index: DESCRIPTION
===
--- DESCRIPTION (revision 77902)
+++ DESCRIPTION (working copy)
@@ -1,10 +1,10 @@
Package: AnnotationHubServer
Title: AnnotationHub Server component
-Version: 0.1.3
+Version: 0.1.4
Author: Dan Tenenbaum
Maintainer: Bioconductor Package Maintainer
Description: AnnotationHub Server component
-Depends: AnnotationHubData
+Depends: AnnotationHubData (>= 0.0.37)
Imports: FastRWeb, methods, rmongodb, rjson, IRanges, parallel,
futile.logger, knitr, parallel
Suggests: RUnit, BiocGenerics, knitr
Dan
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper
>
> [[alternative HTML version deleted]]
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] AnnotationHubServer requires AnnotationHubData of a particular vintage
I've been having this problem for a while with the package:
tim@tim-ThinkPad-T420s:~/bioc-devel$ more
/home/tim/bioc-devel/AnnotationHubServer.Rcheck/00install.out
* installing *source* package AnnotationHubServer ...
** R
** inst
** preparing package for lazy loading
Error in match.fun(FUN) : node stack overflow
ERROR: lazy loading failed for package AnnotationHubServer
* removing
/home/tim/bioc-devel/AnnotationHubServer.Rcheck/AnnotationHubServer
This morning it dawned on me that perhaps installing AnnotationHubData was
a prerequisite, so I gave it a shot:
[1] Creating log directory /home/tim/.AnnotationHubData
* DONE (AnnotationHubData)
tim@tim-ThinkPad-T420s:~/bioc-devel$ R CMD INSTALL AnnotationHubServer/*
installing to library /usr/lib64/R/library
* installing *source* package AnnotationHubServer ...
** R
** inst
** preparing package for lazy loading
rmongodb package (mongo-r-driver) loaded
Use 'help("mongo")' to get started.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
rmongodb package (mongo-r-driver) loaded
Use 'help("mongo")' to get started.
* DONE (AnnotationHubServer)
So perhaps that should go in the DESCRIPTION file for the latter, along
with a revision number? It would seem that I must have had
AnnotationHubData from an older vintage installed, but said older vintage
was not satisfactory, thus, error.
Anyways. Just in case anyone else has the same issue, here it is.
--
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] problem installing biocLite package
Hello,
I initially sent this email to the regular bioconductor mailing list
but they told me I probably should sent it here.
I'm installing some bioclite packages for one of our users. Config
params are
R version: 3.0.1
build with: intel composerxe version 13 using mkl
I installed using the info on the website. The first two steps are
executed without error
|
source("http://bioconductor.org/biocLite.R";)
biocLite()|
However, when I try to execute the command
biocLite('edgeR')
I get the error messages below.
NOTE, when I used a gnu non-mkl version of R 3.0.1 I was able to install
everything without any problem:
output of "biocLite('edgeR')":
> biocLite('edgeR')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
Installing package(s) 'edgeR'
trying URL
'http://bioconductor.org/packages/2.12/bioc/src/contrib/edgeR_3.2.3.tar.gz'
Content type 'application/x-gzip' length 1211896 bytes (1.2 Mb)
opened URL
==
downloaded 1.2 Mb
* installing *source* package 'edgeR' ...
** libs
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_exact_test_by_deviance.cpp -o
R_exact_test_by_deviance.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_loess_by_col.cpp -o R_loess_by_col.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_cr_adjust.cpp -o R_cr_adjust.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_levenberg.cpp -o R_levenberg.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_one_group.cpp -o R_one_group.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c R_simple_good_turing.cpp -o R_simple_good_turing.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c core/adj_coxreid.cpp -o core/adj_coxreid.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c core/glm_levenberg.cpp -o core/glm_levenberg.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c core/glm_one_group.cpp -o core/glm_one_group.o
icpc -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include -DNDEBUG
-I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3 -g
-fp-model precise -c core/interpolator.cpp -o core/interpolator.o
icc -std=gnu99 -I/g/software/R/3.0.1/intelv13-mkl/lib64/R/include
-DNDEBUG -I./core -I. -I/usr/local/include-fpic -xHost -openmp -O3
-g -fp-model precise -c core/fmm_spline.c -o core/fmm_spline.o
icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o
R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o
R_one_group.o R_simple_good_turing.o core/adj_coxreid.o
core/glm_levenberg.o core/glm_one_group.o core/interpolator.o
core/fmm_spline.o -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport
-lifcoremt -limf -lsvml -lm -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
/g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/libimf.so:
warning: warning: feupdateenv is not implemented and will always fail
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In
function `_start':
(.text+0x20): undefined reference to `main'
R_exact_test_by_deviance.o: In function `R_exact_test_by_deviance':
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:19:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:19:
undefined reference to `Rf_isInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:20:
undefined reference to `Rf_isReal'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:22:
undefined reference to `Rf_asInteger'
/scratch/pennings/tmp/Rtmp8dpzIj/R.INSTALL4cc27a4fb944/edgeR/src/R_exact_test_by_deviance.cpp:22:
undefine
Re: [Bioc-devel] BiocParallel: BatchJobs backend (Was: Re: BiocParallel)
Hi Henrik, Sorry for the late response. Suggestions and feedback are always welcome. I just forgot to enable the issue tracker (now enabled). For prototyping I usually use Interactive/Multicore, but I'll regularly test on our local clusters which use Torque or Slurm, respectively. Michel 2013/6/7 Henrik Bengtsson : > Great - this looks promising already. > > What's your test system(s), beyond standard SSH and multicore > clusters? I'm on a Torque/PBS system. > > I'm happy to test, give feedback etc. I don't see an 'Issues' tab on > the GitHub page. Michel, how do you prefer to get feedback? > > /Henrik > > > On Thu, Jun 6, 2013 at 5:21 PM, Michael Lawrence > wrote: >> And here is the on-going development of the backend: >> https://github.com/mllg/BiocParallel/tree/batchjobs >> >> Not sure how well it's been tested. >> >> Kudos to Michel Lang for making so much progress so quickly. >> >> Michael >> >> On Thu, Jun 6, 2013 at 1:59 PM, Dan Tenenbaum wrote: >>> >>> On Thu, Jun 6, 2013 at 1:56 PM, Henrik Bengtsson >>> wrote: >>> > Hi, I'd like to pick up the discussion on a BatchJobs backend for >>> > BiocParallel where it was left back in Dec 2012 (Bioc-devel thread >>> > 'BiocParallel' >>> > [https://stat.ethz.ch/pipermail/bioc-devel/2012-December/003918.html]). >>> > >>> > Florian, would you mind sharing your BatchJobs backend code? Is it >>> > independent of BiocParallel and/or have you tried it with the most >>> > recent BiocParallel implementation >>> > [https://github.com/Bioconductor/BiocParallel/]? >>> > >>> >>> You should be aware that there is Google Summer of Code project in >>> progress to address this. >>> >>> http://www.bioconductor.org/developers/gsoc2013/ (towards the bottom) >>> >>> Dan >>> >>> >>> > /Henrik >>> > >>> > On Tue, Dec 4, 2012 at 12:38 PM, Henrik Bengtsson >>> > wrote: >>> >> Thanks. >>> >> >>> >> On Tue, Dec 4, 2012 at 3:47 AM, Vincent Carey >>> >> wrote: >>> >>> I have been booked up so no chance to deploy but I do have access to >>> >>> SGE and >>> >>> LSF so will try and will report ASAP. >>> >> >>> >> ...and I'll try it out on PBS (... but I most likely won't have time >>> >> to do this until the end of the year). >>> >> >>> >> Henrik >>> >> >>> >>> >>> >>> >>> >>> On Tue, Dec 4, 2012 at 4:08 AM, Hahne, Florian >>> >>> >>> >>> wrote: >>> >>> Hi Henrik, >>> I have now come up now with a relatively generic version of this >>> SGEcluster approach. It does indeed use BatchJobs under the hood and >>> should thus support all available cluster queues, assuming that the >>> necessary batchJobs routines are available. I could only test this on >>> our >>> SGE cluster, but Vince wanted to try other queuing systems. Not sure >>> how >>> far he got. For now the code is wrapped in a little package called >>> Qcluster with some documentation. If you want to I can send you a >>> version >>> in a separate mail. Would be good to test this on other systems, and >>> I am >>> sure there remain some bugs that need to be ironed out. In particular >>> the >>> fault tolerance you mentioned needs to be addressed properly. >>> Currently >>> the code may leave unwanted garbage if things fail in the wrong >>> places >>> because all the communication is file-based. >>> Martin, I'll send you my updated version in case you want to include >>> this >>> in biocParallel for others to contribute. >>> Florian >>> -- >>> >>> >>> >>> >>> >>> >>> On 12/4/12 5:46 AM, "Henrik Bengtsson" wrote: >>> >>> >Picking up this thread in lack of other places (= were should >>> >BiocParallel be discussed?) >>> > >>> >I saw Martin's updates on the BiocParallel - great. Florian's SGE >>> >scheduler was also mentioned; is that one built on top of BatchJobs? >>> >If so I'd be interested in looking into that/generalizing that to >>> > work >>> >with any BatchJobs scheduler. >>> > >>> >I believe there is going to be a new release of BatchJobs rather >>> > soon, >>> >so it's probably worth waiting until that is available. >>> > >>> >The main use case I'm interested in is to launch batch jobs on a >>> >PBS/Torque cluster, and then use multicore processing on each >>> > compute >>> >node. It would be nice to be able to do this using the BiocParallel >>> >model, but maybe it is too optimistic to get everything to work >>> > under >>> >same model. Also, as Vince hinted, fault tolerance etc needs to be >>> >addressed and needs to be addressed differently in the different >>> >setups. >>> > >>> >/Henrik >>> > >>> >On Tue, Nov 20, 2012 at 6:59 AM, Ramon Diaz-Uriarte >>> > >>> >wrote: >>> >> >>> >> >>> >> >>> >> On Sat, 17 Nov 2012 13:05:29 -0800,"Ryan C. Thompson" >>> >> wrote: >>> >> >>>
