date:20170727

[Bioc-devel] Catching SVN up to Github

2017-07-27 Thread Matt Richards

Hi all,

Since our package, "trena", was accepted, we've made some pretty extensive
changes to the package on Github. Our version has so far jumped from
0.99.10 to 0.99.135. These changes are all contained on a forked version of
the Bioconductor mirror, as specified (https://www.bioconductor.org/
developers/how-to/git-mirrors/). We haven't yet put these changes onto SVN.

My question is regarding how to get the Github repo and the SVN on the same
page. I've followed the procedure outlined on the linked page and also
tried the cherry picking procedure, but any `git svn` command
(info/rebase/dcommit) run on the devel branch returns me the same message:

Unable to determine upstream SVN information from HEAD history.

I've also tried a `git svn log`, which returns: fatal: your current branch
appears to be broken

Any ideas what's going on here? I'm a self-admitted novice when it comes to
SVN.

Thanks
Matt

-- 
Matthew Richards
Postdoctoral Fellow
Institute for Systems Biology

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[Bioc-devel] Default Coverage Value

2017-07-27 Thread Dario Strbenac

Hello,

The coverage function is still inconvenient to use with a vector of weights to 
convert a GRanges metadata column into a RleList object.

"The coverage method for GRanges could gain a default value argument."
- Michael Lawrence, January 2013.

"Something like coverage(foo, bar, ..., NA.value=-1)?"
- Tim Triche, Jr., January 2013.

Might this plan be restored (with a default value of 0 for backwards 
compatibility)?

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Rd] matrices with names

2017-07-27 Thread Suzen, Mehmet

Not always, see what happens with lapply:
> x<-matrix(12,1,1)
> names(x)<-"one"
> y<-matrix(1,1,1)
> names(y)<-"one"
> dput(lapply(x,`+`,e2=y))
structure(list(one = structure(13, .Dim = c(1L, 1L))), .Names = "one")
>dput(lapply(x,`+`,e2=1))
structure(list(one = 13), .Names = "one")


Prof. Ripley has pointed out this some time ago:
https://stat.ethz.ch/pipermail/r-devel/2011-October/062297.html

Note that ?`+` tells:

 The rules for determining the attributes of the result are rather
 complicated.  Most attributes are taken from the longer argument.
 Names will be copied from the first if it is the same length as
 the answer, otherwise from the second if that is.  If the
 arguments are the same length, attributes will be copied from
 both, with those of the first argument taking precedence when the
 same attribute is present in both arguments. For time series,
 these operations are allowed only if the series are compatible,
 when the class and ‘tsp’ attribute of whichever is a time series
 (the same, if both are) are used.  For arrays (and an array
 result) the dimensions and dimnames are taken from first argument
 if it is an array, otherwise the second.

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Re: [Bioc-devel] git transition for projects with prior git history

2017-07-27 Thread Vladimir Kiselev

Hi Andrew,

I solved it by just adding '--allow-unrelated-histories' to force the merge:
https://stackoverflow.com/questions/37937984/git-refusing-to-merge-unrelated-histories

Cheers,
Vlad

On Thu, Jul 27, 2017 at 9:53 PM McDavid, Andrew <
andrew_mcda...@urmc.rochester.edu> wrote:

> Is there a recommended recipe to utilize the git.bioconductor.org<
> http://git.bioconductor.org> remote with an existing git repo that has
> non-zero history?  I tried adding the git.bioconductor.org<
> http://git.bioconductor.org> as a remote, making a branch, and then
> checking out a branch on that remote, but it gave my computer sad.  Do I
> need to clone a new repo instead?
>
> Example:
> $ git remote -vv
> bioc https://github.com/Bioconductor-mirror/MAST.git (fetch)
> bioc https://github.com/Bioconductor-mirror/MAST.git (push)
> biocgit 
> g...@git.bioconductor.org:packages/MAST
> (fetch)
> biocgit 
> g...@git.bioconductor.org:packages/MAST
> (push)
> origin g...@github.com:RGLab/MAST.git (fetch)
> origin g...@github.com:RGLab/MAST.git (push
>
> $ git fetch biocgit
> $ git checkout -b bgMaster --track biocgit/master
> ...
> 
> ...
> $ git merge master bgMaster
> fatal: refusing to merge unrelated histories
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
-- 
http://genat.uk

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[Bioc-devel] git transition for projects with prior git history

2017-07-27 Thread McDavid, Andrew

Is there a recommended recipe to utilize the 
git.bioconductor.org remote with an existing git 
repo that has non-zero history?  I tried adding the 
git.bioconductor.org as a remote, making a branch, 
and then checking out a branch on that remote, but it gave my computer sad.  Do 
I need to clone a new repo instead?

Example:
$ git remote -vv
bioc https://github.com/Bioconductor-mirror/MAST.git (fetch)
bioc https://github.com/Bioconductor-mirror/MAST.git (push)
biocgit 
g...@git.bioconductor.org:packages/MAST 
(fetch)
biocgit 
g...@git.bioconductor.org:packages/MAST (push)
origin g...@github.com:RGLab/MAST.git (fetch)
origin g...@github.com:RGLab/MAST.git (push

$ git fetch biocgit
$ git checkout -b bgMaster --track biocgit/master
...

...
$ git merge master bgMaster
fatal: refusing to merge unrelated histories

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Re: [R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file

2017-07-27 Thread Phil Chalmers

Thanks, Duncan. The tarball was created using the standard R CMD build
function. But, as far as I can tell, I must have built the tarball with a
previous R version (e.g., version 3.3), which did not contain the
partial.rdb file when constructing the tarball, and then checked with the
dev version. For some reason my check didn't flag this missing file
locally; but, I suppose mixing and matching R command line versions is a
dangerous game to play anyway.

Moral: always check AND build the package for CRAN with the latest dev, as
even the build process may have changed.

Phil

On Thu, Jul 27, 2017 at 8:34 AM, Duncan Murdoch 
wrote:

> On 26/07/2017 12:23 PM, Phil Chalmers wrote:
>
>> Yes, I can see the partial.rdb file in the list, also in entry 28. So I
>> believe the problem is on the CRAN build.
>>
>
> For the rest of the list:  This claim is incorrect.  The tarball that was
> submitted to CRAN did not contain the partial.rdb file.  The CRAN message
> was correct.
>
> Phil, it would be helpful if you explained how you really produced that
> tarball, so people know how not to do it.
>
> Duncan Murdoch
>
>
>> Phil
>>
>> On Wed, Jul 26, 2017 at 10:30 AM, Duncan Murdoch
>> > wrote:
>>
>> On 26/07/2017 9:05 AM, Phil Chalmers wrote:
>>
>> Hi Duncan,
>>
>> I use the standard R CMD build/check --as-cran combo. Here's my
>> output
>> from my Win 10 64-bit box:
>>
>> C:\Users\Phil\Desktop>C:/PROGRA~1/R/R-devel/bin/x64/R CMD build
>> mirtCAT
>> * checking for file 'mirtCAT/DESCRIPTION' ... OK
>> * preparing 'mirtCAT':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * installing the package to process help pages
>> * saving partial Rd database
>> * creating vignettes ... OK
>> * cleaning src
>> * checking for LF line-endings in source and make files and
>> shell scripts
>> * checking for empty or unneeded directories
>> * building 'mirtCAT_1.6.tar.gz'
>>
>>
>> C:\Users\Phil\Desktop>C:/PROGRA~1/R/R-devel/bin/x64/R CMD check
>> mirtCAT_1.6.tar.gz --as-cran
>> * using log directory 'C:/Users/Phil/Desktop/mirtCAT.Rcheck'
>> * using R Under development (unstable) (2017-07-25 r72968)
>> * using platform: x86_64-w64-mingw32 (64-bit)
>> * using session charset: ISO8859-1
>> * using option '--as-cran'
>> * checking for file 'mirtCAT/DESCRIPTION' ... OK
>> * checking extension type ... Package
>> * this is package 'mirtCAT' version '1.6'
>> * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
>> Maintainer: 'Phil Chalmers > 
>> >
>> >>'
>>
>> * checking package namespace information ... OK
>> * checking package dependencies ... OK
>> * checking if this is a source package ... OK
>> * checking if there is a namespace ... OK
>> * checking for executable files ... OK
>> * checking for hidden files and directories ... OK
>> * checking for portable file names ... OK
>> * checking whether package 'mirtCAT' can be installed ... OK
>> * checking installed package size ... OK
>> * checking package directory ... OK
>> * checking 'build' directory ... OK
>> * checking DESCRIPTION meta-information ... OK
>> * checking top-level files ... OK
>> * checking for left-over files ... OK
>> * checking index information ... OK
>> * checking package subdirectories ... OK
>> * checking R files for non-ASCII characters ... OK
>> * checking R files for syntax errors ... OK
>> * checking whether the package can be loaded ... OK
>> * checking whether the package can be loaded with stated
>> dependencies ... OK
>> * checking whether the package can be unloaded cleanly ... OK
>> * checking whether the namespace can be loaded with stated
>> dependencies
>> ... OK
>> * checking whether the namespace can be unloaded cleanly ... OK
>> * checking loading without being on the library search path ... OK
>> * checking use of S3 registration ... OK
>> * checking dependencies in R code ... OK
>> * checking S3 generic/method consistency ... OK
>> * checking replacement functions ... OK
>> * checking foreign function calls ... OK
>> * checking R code for possible problems ... OK
>> * checking Rd files ... OK
>> * checking Rd metadata ... OK
>> * checking Rd line widths ... OK
>> * checking Rd cross-references ... OK
>> * checking for missing

Re: [R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file

2017-07-27 Thread Duncan Murdoch

On 26/07/2017 12:23 PM, Phil Chalmers wrote:

Yes, I can see the partial.rdb file in the list, also in entry 28. So I
believe the problem is on the CRAN build.

For the rest of the list:  This claim is incorrect.  The tarball that 
was submitted to CRAN did not contain the partial.rdb file.  The CRAN 
message was correct.

Phil, it would be helpful if you explained how you really produced that 
tarball, so people know how not to do it.

Duncan Murdoch

Phil

On Wed, Jul 26, 2017 at 10:30 AM, Duncan Murdoch
> wrote:

On 26/07/2017 9:05 AM, Phil Chalmers wrote:

Hi Duncan,

I use the standard R CMD build/check --as-cran combo. Here's my
output
from my Win 10 64-bit box:

C:\Users\Phil\Desktop>C:/PROGRA~1/R/R-devel/bin/x64/R CMD build
mirtCAT
* checking for file 'mirtCAT/DESCRIPTION' ... OK
* preparing 'mirtCAT':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and
shell scripts
* checking for empty or unneeded directories
* building 'mirtCAT_1.6.tar.gz'

C:\Users\Phil\Desktop>C:/PROGRA~1/R/R-devel/bin/x64/R CMD check
mirtCAT_1.6.tar.gz --as-cran
* using log directory 'C:/Users/Phil/Desktop/mirtCAT.Rcheck'
* using R Under development (unstable) (2017-07-25 r72968)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'mirtCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mirtCAT' version '1.6'
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: 'Phil Chalmers 
>>'

* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mirtCAT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated
dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated
dependencies
... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS)
... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking

Re: [Bioc-devel] xcms adjustRtime-obiwarp Error

2017-07-27 Thread Rainer Johannes

Dear Riccardo,

I will look closer into this. In the meantime it might help if you try a 
different binSize in the ObiwarpParam. Also, could you please add an issue with 
this error on https://github.com/sneumann/xcms ? I can then track and relate 
all changes to the issue.

thanks, jo

On 27 Jul 2017, at 12:56, Riccardo Romoli 
> wrote:

Dear xcms devel,
running the latest stable xcms version I get the following error:

> xod <- adjustRtime(xod, param = ObiwarpParam())
Sample number 3 used as center sample.
Aligning pl55_06h_01.mzXML against pl55_03h_01.mzXML ...
Error: BiocParallel errors
 element index: 1, 2, 3, 4, 5
 first error: Dimensions of profile matrices of files pl55_03h_01.mzXML and 
pl4_01.mzXML do not match!


This is the traceback:

> traceback()
9: stop(.error_bplist(res))
8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
6: bplapply(objL, function(z, cntr, cntrPr, parms) {
  message("Aligning ", basename(fileNames(z)), " against ",
  basename(fileNames(cntr)), " ... ", appendLF = FALSE)
  suppressMessages(curP <- profMat(z, method = "bin", step = binSize(parms),
  returnBreaks = TRUE)[[1]])
  scantime1 <- unname(rtime(cntr))
  scantime2 <- unname(rtime(z))
  mstdiff <- median(c(diff(scantime1), diff(scantime2)))
  mst1 <- which(diff(scantime1) > 5 * mstdiff)[1]
  if (!is.na(mst1)) {
  scantime1 <- scantime1[seq_len((mst1 - 1))]
  message("Found gaps in scan times of the center sample: cut ",
  "scantime-vector at ", scantime1[mst1], " seconds.")
  }
  mst2 <- which(diff(scantime2) > 5 * mstdiff)[1]
  if (!is.na(mst2)) {
  scantime2 <- scantime2[seq_len((mst2 - 1))]
  message("Found gaps in scan time of file ", basename(fileNames(z)),
  ": cut scantime-vector at ", scantime2[mst2], " seconds.")
  }
  rtmaxdiff <- abs(diff(c(scantime1[length(scantime1)], 
scantime2[length(scantime2)])))
  if (rtmaxdiff > (5 * mstdiff)) {
  rtmax <- min(scantime1[length(scantime1)], 
scantime2[length(scantime2)])
  scantime1 <- scantime1[scantime1 <= rtmax]
  scantime2 <- scantime2[scantime2 <= rtmax]
  }
  valscantime1 <- length(scantime1)
  valscantime2 <- length(scantime2)
  if (ncol(cntrPr$profMat) > valscantime1) {
  cntrPr$profMat <- cntrPr$profMat[, -c((valscantime1 +
  1):ncol(cntrPr$profMat))]
  }
  if (ncol(curP$profMat) > valscantime2) {
  curP$profMat <- curP$profMat[, -c((valscantime2 + 
1):ncol(curP$profMat))]
  }
  mzr1 <- c(cntrPr$breaks[1], cntrPr$breaks[length(cntrPr$breaks) -
  1])
  mzr2 <- c(curP$breaks[1], curP$breaks[length(curP$breaks) -
  1])
  mzmin <- min(c(mzr1[1], mzr2[1]))
  mzmax <- max(c(mzr1[2], mzr2[2]))
  mzs <- seq(mzmin, mzmax, by = binSize(parms))
  if (mzmin < mzr1[1]) {
  tmp <- matrix(0, (length(seq(mzmin, mzr1[1], binSize(parms))) -
  1), ncol = ncol(cntrPr$profMat))
  cntrPr$profMat <- rbind(tmp, cntrPr$profMat)
  }
  if (mzmax > mzr1[2]) {
  tmp <- matrix(0, (length(seq(mzr1[2], mzmax, binSize(parms))) -
  1), ncol = ncol(cntrPr$profMat))
  cntrPr$profMat <- rbind(cntrPr$profMat, tmp)
  }
  if (mzmin < mzr2[1]) {
  tmp <- matrix(0, (length(seq(mzmin, mzr2[1], binSize(parms))) -
  1), ncol = ncol(curP$profMat))
  curP$profMat <- rbind(tmp, curP$profMat)
  }
  if (mzmax > mzr2[2]) {
  tmp <- matrix(0, (length(seq(mzr2[2], mzmax, binSize(parms))) -
  1), ncol = ncol(curP$profMat))
  curP$profMat <- rbind(curP$profMat, tmp)
  }
  mzvals <- length(mzs)
  cntrVals <- length(cntrPr$profMat)
  curVals <- length(curP$profMat)
  if ((mzvals * valscantime1) != cntrVals | (mzvals * valscantime2) !=
  curVals | cntrVals != curVals)
  stop("Dimensions of profile matrices of files ", 
basename(fileNames(cntr)),
  " and ", basename(fileNames(z)), " do not match!")
  rtadj <- .Call("R_set_from_xcms", valscantime1, scantime1,
  mzvals, mzs, cntrPr$profMat, valscantime2, scantime2,
  mzvals, mzs, curP$profMat, response(parms), distFun(parms),
  gapInit(parms), gapExtend(parms), factorDiag(parms),
  factorGap(parms), as.numeric(localAlignment(parms)),
  initPenalty(parms))
  if (length(rtime(z)) > valscantime2) {
  rtadj <- c(rtadj, rtime(z)[(valscantime2 + 1):length(rtime(z))])
  warning(basename(fileNames(z)), " :could only align up to a ",
  "retention time of ", rtime(z)[valscantime2], " seconds. ",
  "After that raw retention times are reported.")
  }
  message("OK")
  return(rtadj)
  }, cntr = centerObject, cntrPr = profCtr, parms =

[Bioc-devel] xcms adjustRtime-obiwarp Error

2017-07-27 Thread Riccardo Romoli


Dear xcms devel,
running the latest stable xcms version I get the following error:

> xod <- adjustRtime(xod, param = ObiwarpParam())
Sample number 3 used as center sample.
Aligning pl55_06h_01.mzXML against pl55_03h_01.mzXML ...
Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5
  first error: Dimensions of profile matrices of files 
pl55_03h_01.mzXML and pl4_01.mzXML do not match!



This is the traceback:

> traceback()
9: stop(.error_bplist(res))
8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
6: bplapply(objL, function(z, cntr, cntrPr, parms) {
   message("Aligning ", basename(fileNames(z)), " against ",
   basename(fileNames(cntr)), " ... ", appendLF = FALSE)
   suppressMessages(curP <- profMat(z, method = "bin", step = 
binSize(parms),

   returnBreaks = TRUE)[[1]])
   scantime1 <- unname(rtime(cntr))
   scantime2 <- unname(rtime(z))
   mstdiff <- median(c(diff(scantime1), diff(scantime2)))
   mst1 <- which(diff(scantime1) > 5 * mstdiff)[1]
   if (!is.na(mst1)) {
   scantime1 <- scantime1[seq_len((mst1 - 1))]
   message("Found gaps in scan times of the center sample: cut ",
   "scantime-vector at ", scantime1[mst1], " seconds.")
   }
   mst2 <- which(diff(scantime2) > 5 * mstdiff)[1]
   if (!is.na(mst2)) {
   scantime2 <- scantime2[seq_len((mst2 - 1))]
   message("Found gaps in scan time of file ", 
basename(fileNames(z)),

   ": cut scantime-vector at ", scantime2[mst2], " seconds.")
   }
   rtmaxdiff <- abs(diff(c(scantime1[length(scantime1)], 
scantime2[length(scantime2)])))

   if (rtmaxdiff > (5 * mstdiff)) {
   rtmax <- min(scantime1[length(scantime1)], 
scantime2[length(scantime2)])

   scantime1 <- scantime1[scantime1 <= rtmax]
   scantime2 <- scantime2[scantime2 <= rtmax]
   }
   valscantime1 <- length(scantime1)
   valscantime2 <- length(scantime2)
   if (ncol(cntrPr$profMat) > valscantime1) {
   cntrPr$profMat <- cntrPr$profMat[, -c((valscantime1 +
   1):ncol(cntrPr$profMat))]
   }
   if (ncol(curP$profMat) > valscantime2) {
   curP$profMat <- curP$profMat[, -c((valscantime2 + 
1):ncol(curP$profMat))]

   }
   mzr1 <- c(cntrPr$breaks[1], cntrPr$breaks[length(cntrPr$breaks) -
   1])
   mzr2 <- c(curP$breaks[1], curP$breaks[length(curP$breaks) -
   1])
   mzmin <- min(c(mzr1[1], mzr2[1]))
   mzmax <- max(c(mzr1[2], mzr2[2]))
   mzs <- seq(mzmin, mzmax, by = binSize(parms))
   if (mzmin < mzr1[1]) {
   tmp <- matrix(0, (length(seq(mzmin, mzr1[1], binSize(parms))) -
   1), ncol = ncol(cntrPr$profMat))
   cntrPr$profMat <- rbind(tmp, cntrPr$profMat)
   }
   if (mzmax > mzr1[2]) {
   tmp <- matrix(0, (length(seq(mzr1[2], mzmax, binSize(parms))) -
   1), ncol = ncol(cntrPr$profMat))
   cntrPr$profMat <- rbind(cntrPr$profMat, tmp)
   }
   if (mzmin < mzr2[1]) {
   tmp <- matrix(0, (length(seq(mzmin, mzr2[1], binSize(parms))) -
   1), ncol = ncol(curP$profMat))
   curP$profMat <- rbind(tmp, curP$profMat)
   }
   if (mzmax > mzr2[2]) {
   tmp <- matrix(0, (length(seq(mzr2[2], mzmax, binSize(parms))) -
   1), ncol = ncol(curP$profMat))
   curP$profMat <- rbind(curP$profMat, tmp)
   }
   mzvals <- length(mzs)
   cntrVals <- length(cntrPr$profMat)
   curVals <- length(curP$profMat)
   if ((mzvals * valscantime1) != cntrVals | (mzvals * 
valscantime2) !=

   curVals | cntrVals != curVals)
   stop("Dimensions of profile matrices of files ", 
basename(fileNames(cntr)),

   " and ", basename(fileNames(z)), " do not match!")
   rtadj <- .Call("R_set_from_xcms", valscantime1, scantime1,
   mzvals, mzs, cntrPr$profMat, valscantime2, scantime2,
   mzvals, mzs, curP$profMat, response(parms), distFun(parms),
   gapInit(parms), gapExtend(parms), factorDiag(parms),
   factorGap(parms), as.numeric(localAlignment(parms)),
   initPenalty(parms))
   if (length(rtime(z)) > valscantime2) {
   rtadj <- c(rtadj, rtime(z)[(valscantime2 + 1):length(rtime(z))])
   warning(basename(fileNames(z)), " :could only align up to a ",
   "retention time of ", rtime(z)[valscantime2], " seconds. ",
   "After that raw retention times are reported.")
   }
   message("OK")
   return(rtadj)
   }, cntr = centerObject, cntrPr = profCtr, parms = param)
5: bplapply(objL, function(z, cntr, cntrPr, parms) {
   message("Aligning ", basename(fileNames(z)), " against ",
   basename(fileNames(cntr)), " ... ", appendLF = FALSE)
   suppressMessages(curP <- profMat(z, method = "bin", step = 
binSize(parms),

   returnBreaks =

[Bioc-devel] Vignette for xcms fails to build on tokay1

2017-07-27 Thread Rainer Johannes

Dear all,

one of the xcms vignettes fails to build on tokay1 recently with the error 
message:

Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" 
--quiet --pdf "xcmsDirect.tex" --max-iterations=20 -I 
"C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I 
"C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for 
vignette with name 'xcmsDirect'. The following files exist in directory '.': 
'FlowChart.graffle', 'FlowChart.pdf', 'benchmarking.Rmd-notrun', 
'biomed-central.csl', 'example.tsv', 'new_functionality.R', 
'new_functionality.Rmd', 'new_functionality.html', 'new_functionality.org', 
'references.bib', 'xcms.bib', 'xcms.org', 
'xcmsDirect-005.pdf', 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw', 
'xcmsMSn.Rnw', 'xcmsPreprocess.Rnw-notrun'
Calls:  -> find_vignette_product
Execution halted

is this some problem with tokay1 or is it related to the vignette (I have no 
problems building this vignette in my Windows build machine)?

thanks, jo


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Re: [Rd] dir.create typo in manual An Introduction to R

2017-07-27 Thread Martin Maechler

> John Blischak 
> on Wed, 26 Jul 2017 16:22:22 -0500 writes:

> In the section FIles and Directories in the manual An Introduction to
> R it refers to the function create.dir:

> 
https://cran.r-project.org/doc/manuals/r-devel/R-intro.html#Files-and-directories

> I've attached a patch against revision 72974 to change this to dir.create.

Thank you, John! -- fixed in the sources now.
Martin

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Re: [Bioc-devel] xcms adjustRtime-obiwarp Error

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[Bioc-devel] Vignette for xcms fails to build on tokay1

Re: [Rd] dir.create typo in manual An Introduction to R

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