Re: [Bioc-devel] Changing a name of a package already under review
Thank you everyone I will ask @lshep! On Tue, Oct 23, 2018 at 4:09 AM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Yes it is possible to change the name of the package while under review. > You will need to change your github repository first. Then update the > github link and the issue name on the review. We will need to also make > the change on our database of new issues. When the issue is renamed please > ask @lshep on the issue number to rename the issue before making any > additional version bumps to the package. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Turaga, Nitesh > *Sent:* Monday, October 22, 2018 9:08:39 PM > *To:* Lan Huong Nguyen; Shepherd, Lori > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Changing a name of a package already under > review > > It is be possible. While it’s in review, you can change the name of your > package. > > I believe Lori, will have to do some magic to get the Single package > builder to get the correct version. > > Best, > > Nitesh > > > On Oct 22, 2018, at 6:27 PM, Lan Huong Nguyen > wrote: > > > > Hi, > > > > I was wondering if it is possible to change the name of the package which > > is already under review. This is because, after obtaining some commentary > > on the implementation and restructuring my package I thought that another > > name might be appropriate. > > > > Best, > > Lan > > > >[[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. -- -Lan [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Ascona Workshop 2019 -- Statistical Challenges in Medical Data Science, 16–21 June 2019
Save the date! We would like to announce and invite you to the workshop on Statistical Challenges in Medical Data Science, to be held on 16 – 21 June 2019 at Monte Verità, Ascona, Switzerland. The purpose of the workshop is to bring together participants from statistics, computational sciences, biology and medicine, and to encourage interaction in an informal and cooperative atmosphere. Confirmed invited speakers: Karsten Borgwardt (ETH Zurich), Tianxi Cai (Harvard), Christina Curtis (Stanford), Anna Goldenberg (U Toronto), Jennifer Listgarten (UC Berkeley), Marylyn Ritchie (U Penn), Michael Snyder (Stanford), Matthew Stephens (U Chicago), Yinyin Yuan (ICR London). Application will open in January 2019. For more information, please refer to https://www.bsse.ethz.ch/cbg/cbg-news/ascona-2019.html Niko Beerenwinkel (ETH Zurich) Peter Bühlmann (ETH Zurich) Wolfgang Huber (EMBL) ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error building the vignette
Are you using the correct version of R and up-to-date Bioconductor 'devel'
packages? I installed your package from git.bioconductor.org then started R,
tangled the vignette, and sourced the result
> setwd("BioCor/vignettes")
> knitr::purl("BioCor_1_basics.Rmd")
> source("BioCor_1_basics.R", max=Inf, echo=TRUE)
And eventually came to
> goSemSim <- GOSemSim::geneSim("241", "251", semData = hsGO,
+ measure = "Wang", combine="BMA")$geneSim
Error in GOSemSim::geneSim("241", "251", semData = hsGO, measure = "Wang",
(from BioCor_1_basics.R#130) :
$ operator is invalid for atomic vectors
In addition: Warning message:
In mgeneSim(genes, genesReact) : Some genes are not in the list provided.
Looking just a little more I see
> GOSemSim::geneSim("241", "251", semData = hsGO,
> measure = "Wang", combine="BMA")
[1] NA
I didn't look further; it could have to do with recently updated GO.db?
> sessionInfo()
R version 3.5.1 Patched (2018-10-05 r75405)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Users/ma38727/bin/R-3-5-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-3-5-branch/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GOSemSim_2.7.1 reactome.db_1.64.0 org.Hs.eg.db_3.7.0
[4] AnnotationDbi_1.43.1 IRanges_2.15.18 S4Vectors_0.19.23
[7] Biobase_2.41.2 BiocGenerics_0.27.1 BioCor_1.5.5
[10] BiocStyle_2.9.6 BiocManager_1.30.3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 compiler_3.5.1 bitops_1.0-6
[4] tools_3.5.1 digest_0.6.18bit_1.1-14
[7] lattice_0.20-35 annotate_1.59.1 evaluate_0.12
[10] RSQLite_2.1.1memoise_1.1.0pkgconfig_2.0.2
[13] Matrix_1.2-14graph_1.59.2 DBI_1.0.0
[16] yaml_2.2.0 stringr_1.3.1knitr_1.20
[19] rprojroot_1.3-2 bit64_0.9-7 grid_3.5.1
[22] GSEABase_1.43.1 XML_3.98-1.16BiocParallel_1.15.15
[25] rmarkdown_1.10 GO.db_3.7.0 blob_1.1.1
[28] magrittr_1.5 backports_1.1.2 htmltools_0.3.6
[31] xtable_1.8-3 stringi_1.2.4RCurl_1.95-4.11
On 10/25/18, 4:24 AM, "Bioc-devel on behalf of Lluís Revilla"
wrote:
Dear Bioconductor team and list,
I found that my package on devel (BioCor) fails to build on all the OS. The
error message is related to creating figures of the vignette (see below).
I haven't touched the vignettes in a while. and building the package on my
machine passes all the checks. In addition, I found the same type of error
happens to other packages (metagene, and yesterday to restfulSE). I don't
know where to look at to solve this problem. Do you have any recommendation?
Many thanks,
Lluís
PS: Errors on the devel branch:
Linux:
* creating vignettes ... ERROR
Quitting from lines 271-282 (BioCor_1_basics.Rmd)
Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
Windows:
* creating vignettes ... ERROR
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "BioCor_1_basics_files/figure-html/hclust1-1.png" -trim
"BioCor_1_basics_files/figure-html/hclust1-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "BioCor_1_basics_files/figure-html/hclust3-1.png" -trim
"BioCor_1_basics_files/figure-html/hclust3-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "BioCor_1_basics_files/figure-html/hclust3b-1.png" -trim
"BioCor_1_basics_files/figure-html/hclust3b-1.png"' execution failed with
error code 4
Quitting from lines 271-282 (BioCor_1_basics.Rmd)
Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
MacOS
* creating vignettes ... ERROR
sh: line 1: 8065 Abort trap: 6 'convert'
'BioCor_1_basics_files/figure-html/hclust1-1.png' -trim
'BioCor_1_basics_files/figure-html/hclust1-1.png' > /dev/null
sh: line 1: 8098 Abort trap: 6 'convert'
'BioCor_1_basics_files/figure-html/hclust3-1.png' -trim
'BioCor_1_basics_files/figure-html/hclust3-1.png' > /dev/null
sh: line 1: 8163 Abort trap: 6 'convert'
'BioCor_1_basics_files/figure-html/hclust3b-1.png' -trim
'BioCor_1_basics_
[Bioc-devel] Error building the vignette
Dear Bioconductor team and list, I found that my package on devel (BioCor) fails to build on all the OS. The error message is related to creating figures of the vignette (see below). I haven't touched the vignettes in a while. and building the package on my machine passes all the checks. In addition, I found the same type of error happens to other packages (metagene, and yesterday to restfulSE). I don't know where to look at to solve this problem. Do you have any recommendation? Many thanks, Lluís PS: Errors on the devel branch: Linux: * creating vignettes ... ERROR Quitting from lines 271-282 (BioCor_1_basics.Rmd) Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors Windows: * creating vignettes ... ERROR Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BioCor_1_basics_files/figure-html/hclust1-1.png" -trim "BioCor_1_basics_files/figure-html/hclust1-1.png"' execution failed with error code 4 Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BioCor_1_basics_files/figure-html/hclust3-1.png" -trim "BioCor_1_basics_files/figure-html/hclust3-1.png"' execution failed with error code 4 Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "BioCor_1_basics_files/figure-html/hclust3b-1.png" -trim "BioCor_1_basics_files/figure-html/hclust3b-1.png"' execution failed with error code 4 Quitting from lines 271-282 (BioCor_1_basics.Rmd) Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors MacOS * creating vignettes ... ERROR sh: line 1: 8065 Abort trap: 6 'convert' 'BioCor_1_basics_files/figure-html/hclust1-1.png' -trim 'BioCor_1_basics_files/figure-html/hclust1-1.png' > /dev/null sh: line 1: 8098 Abort trap: 6 'convert' 'BioCor_1_basics_files/figure-html/hclust3-1.png' -trim 'BioCor_1_basics_files/figure-html/hclust3-1.png' > /dev/null sh: line 1: 8163 Abort trap: 6 'convert' 'BioCor_1_basics_files/figure-html/hclust3b-1.png' -trim 'BioCor_1_basics_files/figure-html/hclust3b-1.png' > /dev/null Quitting from lines 271-282 (BioCor_1_basics.Rmd) Error: processing vignette 'BioCor_1_basics.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
