Re: [Bioc-devel] pdflatex not found on oaxaca (Mac OS X Mavericks (10.9.5)/x86_64) - R CMD check fails

On 12/04/2016 03:41 AM, Knoll, Max wrote: Hi, I'm stuck in the submission process and encounter the following error when CHECK is performed (on oaxaca): * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

Hi Nan, Zach, Val, On 12/05/2016 01:45 PM, Obenchain, Valerie wrote: Hi, We need to make several updates to the mac machines. These are the last 2 builders that still need to move from the Hutch to RPCI. Because they are still at the Hutch, access to them is limited. We will get to these

Re: [Bioc-devel] biconductor build error and warning

This helps, Thank you so much! From: Herv� Pag�s Sent: Monday, December 5, 2016 9:16:15 PM To: Dwivedi, Bhakti Cc: bioc-devel Subject: Re: [Bioc-devel] biconductor build error and warning Hi Bhakti, Please see my post from October here

Re: [Bioc-devel] biconductor build error and warning

Hi Bhakti, Please see my post from October here https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009997.html for why Rmpfr (and thus HH) fails to install on oaxaca. We're still hoping that the CRAN folks will start providing Mac binary packages for r-devel soon. In the meantime

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

Hi, We need to make several updates to the mac machines. These are the last 2 builders that still need to move from the Hutch to RPCI. Because they are still at the Hutch, access to them is limited. We will get to these updates as soon as we can. Valerie On 12/05/2016 01:27 PM, Dan Tenenbaum

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

Hi Zach and Dan, - thanks a lot for the information, that made things much clearer. >From the build error message, it seems rcdk 3.3.8 only "partially" made to the BioC builds, which means 3.3.8 is available on Linux and Windows, but not Mac (still 3.3.6). Maybe I'll just wait for the Java

Re: [Bioc-devel] split on IRanges semantic change 3.3->3.4

Hi Marcin, I'm not sure I agree with that Stack Overflow answer. Sure, ceiling(1:100/10) is a neat arithmetical trick to get what you want, but it would be a lot more obvious to me at least to use rep(1:10, each=10). And even better to use Partitioning objects when you have IRanges around. If you

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

​Hi Nan, rCDK 3.3.6 requires Java8 and will throw error if the Java environment is incorrect. BioC Build only has Java7 hence the error. The new version of rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on CRAN), these errors should clear up. Please keep me posted if

[Bioc-devel] Query about hgu133plus2 database

Hi, I was trying to get the gene mapping for one of the datasets in Affymetrix. I found a dissimilarity between Affymetrix file and the database in hgu133plus2. As per example, For the probeset "1553011_at", I have found a mapping to both these ENTREZ ID's 6872 /// 138474 in the file

Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)

Hey guys, - it seems this problem is also affecting the other two Bioc packages depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any ideas why? Thanks, -Nan On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao wrote: > Hi Bioc, > > - the Rcpi package depends on

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Hi Jurat, Please read the Writing R Extensions manual if you have not already: https://cran.r-project.org/doc/manuals/r-release/R-exts.html It is quite comprehensive. A gentler introduction is: https://bioconductor.org/developers/how-to/buildingPackagesForBioc/ As for your vignette, note that

Re: [Bioc-devel] split on IRanges semantic change 3.3->3.4

Sorry about that. I pushed a fix to devel (2.9.14) and soon release. Btw, it's not typically a good idea to use a real valued vector as a factor. In this case, you could use %/% or better yet a partitioning, i.e., relist(ir, PartitioningByEnd(seq(10, 100, 10))). Michael On Sun, Dec 4, 2016 at

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Dear Leonardo : Thanks again for your helpful package to resolve my doubt. Through Dan's kind instruction, previous problems are partially solved instead still getting error with vignette compilation. I reproduced example bed files and tried most simplest way to load these data to let vignette

[Bioc-devel] Question, R, get sequence genes

Hi My question is how i can get sequence some genes with " BSgenome.Btaurus.UCSC.bosTau8" i want to get sequence of a list of locations of genes like: chr25 3510245435102482 chr19 4403596944036049 chr18 1044411510444121 chr27 3724030037240538 chr23