[Bioc-devel] Flagme creating vignettes ERROR
Hi, last night I received an automatic message regardless the flagme package (I'm the co-author and the manteiner): o ERROR for 'R CMD build' on zin2. See the details here: http://bioconductor.org/checkResults/3.1/bioc-LATEST/flagme/zin2-buildsrc.html I followed the link above and I see the error: %% ## ## ### ### Running command: ### ### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data flagme ### ## ## * checking for file ‘flagme/DESCRIPTION’ ... OK * preparing ‘flagme’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR ... Error: processing vignette 'flagme.Rnw' failed with diagnostics: chunk 3 (label = addXCMS) Error in x$membership : $ operator not defined for this S4 class Execution halted %-% I downloaded the source of the package and I tried to build it. I get no errors. %-% :~$ R CMD build --keep-empty-dirs --no-resave-data flagme * checking for file ‘flagme/DESCRIPTION’ ... OK * preparing ‘flagme’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building ‘flagme_1.24.0.tar.gz’ %--% What should I do? All the best, Riccardo -- Riccardo Romoli, PhD Mass Spectrometry Centre - CISM University of Florence Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy Phone: +39 055 4573783/2 email: riccardo.rom...@unifi.it web site: www.cism.unifi.it ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
Salut Hervé, It sounds great, but according to the man page, snpsById() requires an 'XtraSNPlocs' object, and the only one availble on bioconductor is 'XtraSNPlocs.Hsapiens.dbSNP141.GRCh38' I need to work with GRCh37 annotations. Is there a trick to transform a 'SNPlocs' object, such as 'SNPlocs.Hsapiens.dbSNP142.GRCh37', into an 'XtraSNPlocs'? Ne remets jamais à demain... :p Cheers, Fred Frederic Commo Bioinformatics, U981 Gustave Roussy De : Hervé Pagès [hpa...@fredhutch.org] Date d'envoi : mercredi 1 juillet 2015 20:25 À : COMMO Frederic; bioc-devel@r-project.org Objet : Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37 Salut Frédéric, I had this on my list for a long time so here it goes. Starting with BSgenome 1.36.2 (in release) and 1.37.3 (in devel), a new API is available for querying a SNPlocs object: snpsBySeqname() snpsByOverlaps() snpsById() Note that this is the new recommended API. In particular snpsById() is what should be used instead of rsid2loc(). It has an argument (ifnotfound) that let's you control what to do if some SNP ids are not found. See ?SNPlocs for more information and some examples. These new versions of BSgenome should become available via biocLite() in 24 hours or so. Let me know if you run into problems. Cheers, H. On 06/29/2015 03:50 AM, COMMO Frederic wrote: Hi, I'm trying to map rsi Ids provided in the Affymetrix cytoScanHD arrays, using the 'SNPlocs.Hsapiens.dbSNP142.GRCh37' package, and rsid2loc(). It turns out that some of these rsi ids are unknown, e.g. rsi7553394, and rsi2loc() fails on the entire search. It would be nice if rsi2loc() would catch the failures, then return the found and the unknown ids, separately, maybe as a list or in success/failure slots. So a multiple-Ids search would not fail. Maybe I missed something, and the function already handle errors. ## To reproduce ## rs7553394 corresponds to probe SNP_A-1780654 in the Affy cytoScanHD, annotated in Hg19. library(SNPlocs.Hsapiens.dbSNP142.GRCh37) rsids - c(rs10458597, rs12565286, rs7553394) rsid2loc(rsids, caching=TRUE) Fred Frederic Commo Bioinformatics, U981 Gustave Roussy [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
Salut Frédéric, As I said, this is available in the new versions of BSgenome (1.36.2 in release, 1.37.3 in devel) which will propagate to the public repos in a couple of hours. So make sure to run biocLite() (with no arguments) in a couple of hours to get any update that will become available today. Then try again. Cheers, H. On 07/02/2015 09:15 AM, COMMO Frederic wrote: Salut Hervé, It sounds great, but according to the man page, snpsById() requires an 'XtraSNPlocs' object, and the only one availble on bioconductor is 'XtraSNPlocs.Hsapiens.dbSNP141.GRCh38' I need to work with GRCh37 annotations. Is there a trick to transform a 'SNPlocs' object, such as 'SNPlocs.Hsapiens.dbSNP142.GRCh37', into an 'XtraSNPlocs'? Ne remets jamais à demain... :p Cheers, Fred Frederic Commo Bioinformatics, U981 Gustave Roussy De : Hervé Pagès [hpa...@fredhutch.org] Date d'envoi : mercredi 1 juillet 2015 20:25 À : COMMO Frederic; bioc-devel@r-project.org Objet : Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37 Salut Frédéric, I had this on my list for a long time so here it goes. Starting with BSgenome 1.36.2 (in release) and 1.37.3 (in devel), a new API is available for querying a SNPlocs object: snpsBySeqname() snpsByOverlaps() snpsById() Note that this is the new recommended API. In particular snpsById() is what should be used instead of rsid2loc(). It has an argument (ifnotfound) that let's you control what to do if some SNP ids are not found. See ?SNPlocs for more information and some examples. These new versions of BSgenome should become available via biocLite() in 24 hours or so. Let me know if you run into problems. Cheers, H. On 06/29/2015 03:50 AM, COMMO Frederic wrote: Hi, I'm trying to map rsi Ids provided in the Affymetrix cytoScanHD arrays, using the 'SNPlocs.Hsapiens.dbSNP142.GRCh37' package, and rsid2loc(). It turns out that some of these rsi ids are unknown, e.g. rsi7553394, and rsi2loc() fails on the entire search. It would be nice if rsi2loc() would catch the failures, then return the found and the unknown ids, separately, maybe as a list or in success/failure slots. So a multiple-Ids search would not fail. Maybe I missed something, and the function already handle errors. ## To reproduce ## rs7553394 corresponds to probe SNP_A-1780654 in the Affy cytoScanHD, annotated in Hg19. library(SNPlocs.Hsapiens.dbSNP142.GRCh37) rsids - c(rs10458597, rs12565286, rs7553394) rsid2loc(rsids, caching=TRUE) Fred Frederic Commo Bioinformatics, U981 Gustave Roussy [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Flagme creating vignettes ERROR
- Original Message -
From: Riccardo Romoli riccardo.rom...@unifi.it
To: bioc-devel@r-project.org
Sent: Thursday, July 2, 2015 2:55:41 AM
Subject: [Bioc-devel] Flagme creating vignettes ERROR
Hi, last night I received an automatic message regardless the flagme
package (I'm the co-author and the manteiner):
o ERROR for 'R CMD build' on zin2. See the details here:
http://bioconductor.org/checkResults/3.1/bioc-LATEST/flagme/zin2-buildsrc.html
I followed the link above and I see the error:
%%
##
##
###
### Running command:
###
### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
--keep-empty-dirs
--no-resave-data flagme
###
##
##
* checking for file ‘flagme/DESCRIPTION’ ... OK
* preparing ‘flagme’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
...
Error: processing vignette 'flagme.Rnw' failed with diagnostics:
chunk 3 (label = addXCMS)
Error in x$membership : $ operator not defined for this S4 class
Execution halted
%-%
I downloaded the source of the package and I tried to build it. I get
no
errors.
%-%
:~$ R CMD build --keep-empty-dirs --no-resave-data flagme
* checking for file ‘flagme/DESCRIPTION’ ... OK
* preparing ‘flagme’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘flagme_1.24.0.tar.gz’
%--%
What should I do?
Are you using R-3.2.1 when you try and build it?
Does your sessionInfo() (package versions) look more or less like this when you
Stangle and source your vignette?
sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] flagme_1.24.0 CAMERA_1.24.0 igraph_1.0.1
[4] xcms_1.44.0 Biobase_2.28.0 ProtGenerics_1.0.0
[7] BiocGenerics_0.14.0 mzR_2.2.1 Rcpp_0.11.6
[10] gcspikelite_1.6.0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 plyr_1.8.3 bitops_1.0-6
[4] tools_3.2.1 rpart_4.1-10digest_0.6.8
[7] gtable_0.1.2lattice_0.20-31 graph_1.46.0
[10] SparseM_1.6 proto_0.3-10gridExtra_0.9.1
[13] stringr_1.0.0 cluster_2.0.2 caTools_1.17.1
[16] gtools_3.5.0stats4_3.2.1grid_3.2.1
[19] nnet_7.3-10 RBGL_1.44.0 survival_2.38-2
[22] foreign_0.8-64 gdata_2.16.1latticeExtra_0.6-26
[25] Formula_1.2-1 ggplot2_1.0.1 reshape2_1.4.1
[28] magrittr_1.5Hmisc_3.16-0scales_0.2.5
[31] gplots_2.17.0 codetools_0.2-11splines_3.2.1
[34] MASS_7.3-41 colorspace_1.2-6KernSmooth_2.23-15
[37] stringi_0.5-5 acepack_1.3-3.3 munsell_0.4.2
Try updating (with biocLite()) so all your packages are the most recent version
and then see if you can reproduce the issue.
Incidentally, here is the traceback from sourcing the stangled vignette:
###
### code chunk number 3: addXCMS
###
pd.2 - peaksDataset(cdfFiles[1:3], mz=seq(50,550), rtrange=c(7.5,8.5))
Reading /home/biocbuild/bbs-3.1-bioc/R/library/gcspikelite/data/0709_468.CDF
Reading /home/biocbuild/bbs-3.1-bioc/R/library/gcspikelite/data/0709_474.CDF
Reading /home/biocbuild/bbs-3.1-bioc/R/library/gcspikelite/data/0709_475.CDF
pd.2 - addXCMSPeaks(cdfFiles[1:3], pd.2, peakPicking=c('mF'),
+ snthresh=3, fwhm=4, step=1, steps=2, mzdiff=0.5)
Start grouping after retention time.
