Re: [Bioc-devel] maftools package not updated after pushing bug fixes.

2017-01-05 Thread Vladimir Kiselev 
Maybe 1.0.4 is smaller than 1.0.30? Try to change to 1.0.31.

On Fri, 6 Jan 2017, 05:32 Anand MT,  wrote:

> Hi Vincent,
>
> Thanks for reply. I swear this was OK till yesterday for updated version!
> This "file not found" issue often occurs but it resolves by itself during
> next builds. Anyways, even when everything was OK, package didn't update to
> newer version.
>
>
>
> 
> From: Vincent Carey 
> Sent: 06 January 2017 08:27:01
> To: Anand MT
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] maftools package not updated after pushing bug
> fixes.
>
>
>
> On Thu, Jan 5, 2017 at 9:33 PM, Anand MT > wrote:
> Hi,
>
>
> I recently pushed few bug fixes and removed some dependency packages which
> were no longer required. I did this a week ago and updated version to 1.0.4
> from 1.0.30.
>
> Build reports are OK for updated version.
>
> http://bioconductor.org/checkResults/release/bioc-LATEST/maftools/
>
> Hi -- there is an error for linux build on that link.
>
>
>
>
> However, release site is still at older 1.0.30. How to proceed now ?
>
> Probably have to fix the build error --
>
>
> Done !
> Quitting from lines 152-153 (maftools.Rmd)
> Error: processing vignette 'maftools.Rmd' failed with diagnostics:
> file not found: /dev/shm/file6fd4ebc7d82
>
> Execution halted
>
>
>
>
> Thank you.
>
> -Anand
>
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>
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[Bioc-devel] readGAlignments Lacks strandMode

2017-01-05 Thread Dario Strbenac 
Good day,

readGAlignmentPairs has strandMode but readGAlignments doesn't, which means 
that single-end strand-specific RNA-seq that generates sequences on the 
opposite strand to the gene needs a subsequent ifelse statement. The API could 
be more consistent by providing a strandMode option for readGAlignments and 
other similar functions in GenomicAlignments.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Rd] strsplit(perl=TRUE), gregexpr(perl=TRUE) very slow for long strings

2017-01-05 Thread William Dunlap via R-devel 
While doing some speed testing I noticed that in R-3.2.3 the perl=TRUE
variants of strsplit() and gregexpr() took time proportional to the
square of the number of pattern matches in their input strings.  E.g.,
the attached test function times gsub, strsplit, and gregexpr, with
perl TRUE (PCRE) and FALSE (TRE), when the input string contains 'n'
matches to the given pattern.  Notice the quadratic (in n) time growth
for the StrSplitPCRE and RegExprPCRE columns.

> regex.perf.test(N=2^(11:20))

  N SubTRE SubPCRE StrSplitTRE StrSplitPCRE RegExprTRE RegExprPCRE

elapsed2048   0.000.000.00 0.00   0.000.00
elapsed4096   0.000.000.01 0.00   0.000.00
elapsed8192   0.000.000.00 0.01   0.000.01
elapsed   16384   0.020.000.00 0.05   0.020.08
elapsed   32768   0.000.000.01 0.16   0.000.29
elapsed   65536   0.020.010.04 0.59   0.010.96
elapsed  131072   0.030.020.08 2.37   0.052.43
elapsed  262144   0.060.040.17 9.58   0.109.61
elapsed  524288   0.140.050.3639.14   0.21   38.58
elapsed 1048576   0.300.080.52   155.50   0.40  155.43

I have not looked at R's code, but it is possible that the problem is
caused by PCRE repeatedly scanning (once per match) the entire input
string to make sure it is valid UTF-8.  If so, adding
PCRE_NO_UTF8_CHECK to the flags given to pcre_exec would solve the
problem.  Perhaps R is already doing that in gsub(perl=TRUE).

Here is the test function:

regex.perf.test <- function(N=c(1e4, 2e4, 4e4, 8e4)) {
  makeTestString <- function(n) paste(collapse="",  rep("ab", n))
  s <- lapply(N, makeTestString)
  fns <- list(SubTRE=function(si) gsub("a", "", si, perl=FALSE),
  SubPCRE=function(si) gsub("a", "", si, perl=TRUE),
  StrSplitTRE=function(si) strsplit(si, "a", perl=FALSE),
  StrSplitPCRE=function(si) strsplit(si, "a", perl=TRUE),
  RegExprTRE=function(si) gregexpr("a", si, perl=FALSE),
  RegExprPCRE=function(si) gregexpr("a", si, perl=TRUE))
  times <- lapply(fns, function(fn) sapply(s, function(si)
system.time(fn(si))["elapsed"]))
  do.call("cbind", c(list(N=N), times))
}

Bill Dunlap
TIBCO Software
wdunlap tibco.com

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Re: [Bioc-devel] maftools package not updated after pushing bug fixes.

2017-01-05 Thread Vincent Carey 
On Thu, Jan 5, 2017 at 9:33 PM, Anand MT  wrote:

> Hi,
>
>
> I recently pushed few bug fixes and removed some dependency packages which
> were no longer required. I did this a week ago and updated version to 1.0.4
> from 1.0.30.
>
> Build reports are OK for updated version.
>
> http://bioconductor.org/checkResults/release/bioc-LATEST/maftools/


Hi -- there is an error for linux build on that link.


>
>
>
> However, release site is still at older 1.0.30. How to proceed now ?
>

Probably have to fix the build error --

Done !
Quitting from lines 152-153 (maftools.Rmd)
Error: processing vignette 'maftools.Rmd' failed with diagnostics:
file not found: /dev/shm/file6fd4ebc7d82

Execution halted



>
>
> Thank you.
>
> -Anand
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] R version-dependent segfault

2017-01-05 Thread Martin Morgan 

On 01/05/2017 11:10 AM, Vladimir Kiselev wrote:

Dear Martin,

Many thanks for your reply, it was really helpful. My collaborator ran
the commands you suggested and got the following output:

*
$ Rscript norm_laplacian.R
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
 'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
 -I/home/jake/miniconda3/include
 -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
-I"/home/jake/Documents"   -fpic  -I/home/jake/miniconda3/include  -c
norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/jake/miniconda3/lib/R/lib
-L/home/jake/miniconda3/lib -lgfortran -o sourceCpp_2.so
norm_laplacian.o -L/home/jake/miniconda3/lib/R/lib -lRlapack
-L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
-L/home/jake/miniconda3/lib/R/lib -lR
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10

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] stats graphics  grDevices utils datasets  base

other attached packages:
[1] Rcpp_0.12.8

loaded via a namespace (and not attached):
[1] tools_3.3.2   RcppArmadillo_0.7.600.1.0

$ g++ --version|head -n1
g++ (Ubuntu 6.2.0-5ubuntu12) 6.2.0 20161005
*

So running the simplified code did not produce a segfault and suggested
that the problem was in SC3::norm_laplacian(). And indeed, running
valgrind with SC3::norm_laplacian(matrix(runif(100), nrow = 10)) did
catch the error:

*
$ R -d valgrind -f norm_laplacian.R
==7046== Memcheck, a memory error detector
==7046== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==7046== Using Valgrind-3.12.0.SVN and LibVEX; rerun with -h for
copyright info
==7046== Command: /home/jake/miniconda3/lib/R/bin/exec/R -f norm_laplacian.R
==7046==

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


library(Rcpp)
sourceCpp("norm_laplacian.cpp", showOutput=TRUE)

/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
 'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
 -I/home/jake/miniconda3/include
 -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
-I"/home/jake/Documents"   -fpic  -I/home/jake/miniconda3/include  -c
norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/jake/miniconda3/lib/R/lib
-L/home/jake/miniconda3/lib -lgfortran -o sourceCpp_2.so
norm_laplacian.o -L/home/jake/miniconda3/lib/R/lib -lRlapack
-L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
-L/home/jake/miniconda3/lib/R/lib -lR

xx <- norm_laplacian(matrix(runif(100), nrow = 10))
SC3::norm_laplacian(matrix(runif(100), nrow = 10))

==7046== Use of uninitialised value of size 8
==7046==at 0x213645B8: direct_max (op_max_meat.hpp:362)
==7046==by 0x213645B8: max (Mat_meat.hpp:6801)
==7046==by 0x213645B8: norm_laplacian(arma::Mat)
(cppFunctions.cpp:87)
==7046==by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)
==7046==by 0x521DE81: R_doDotCall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x522BD99: do_dotcall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267AAC: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526B0A7: do_begin (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526789E: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5268B8C: Rf_applyClosure (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267BBF: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A6C1E: Rf_ReplIteration (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A6DD1: R_ReplConsole (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A8758: run_Rmainloop (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==
==7046== Invalid read of size 8
==7046==at 0x213645B8: direct_max (op_max_meat.hpp:362)
==7046==by 0x213645B8: max (Mat_meat.hpp:6801)
==7046==by 0x213645B8: norm_laplacian(arma::Mat)
(cppFunctions.cpp:87)
==7046==by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)
==7046==by 0x521DE81: R_doDotCall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x522BD99: do_dotcall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267AAC: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526B0A7: do_begin (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526789E: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)

Re: [Bioc-devel] Updating package

2017-01-05 Thread Martin Morgan 

On 01/05/2017 01:25 PM, Charles Determan wrote:

I committed my changes earlier this morning from the 'devel' branch via
the 'git svn dcommit --add-author-from' the website
(https://www.bioconductor.org/developers/how-to/git-mirrors/).  I have
yet to see any changes on the build page though for the `devel`
(http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/).  Did I
miss another step or is the build process reporting slow or perhaps I am
looking in the wrong place still?


builds run nightly, check at the top of the page 
http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/ for the 
date of the svn 'snapshot' and the date the build report is published. 
Currently these are


Snapshot Date: 2017-01-03 17:15:43 -0500 (Tue, 03 Jan 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks
Last Changed Rev: 125601 / Revision: 125601
Last Changed Date: 2017-01-03 17:11:11 -0500 (Tue, 03 Jan 2017)

This page was generated on 2017-01-04 16:34:16 -0500 (Wed, 04 Jan 2017).

You can see here

https://github.com/Bioconductor-mirror/OmicsMarkeR

that your commit is reflected in the mirror of the svn repository, and with

  svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR

  cd OmicsMarkeR
  svn log|head

with output

OmicsMarkeR$   svn log|head

r125696 | c.determan | 2017-01-05 10:31:07 -0500 (Thu, 05 Jan 2017) | 3 
lines


increment sub-sub version for bug fix

From: Charles Determan 

r123124 | hpa...@fhcrc.org | 2016-10-27 18:00:06 -0400 (Thu, 27 Oct 
2016) | 1 line


auxiliary -concordance.tex files don't belong to the package source tree

that your commit has made it to the definitive location, the svn 
repository for your package.


Martin





Regards,
Charles

On Thu, Jan 5, 2017 at 9:47 AM, Charles Determan > wrote:

That seems to have been the issue.  It had been some time since I
needed to commit to bioconductor I forgot my username was
different.  Thank you Martin for pointing that simple problem out.
I have now 'dcommit' my 'devel' branch so if I understand correctly
the changes should be with bioconductor to apply accordingly.

Regards,
Charles

On Thu, Jan 5, 2017 at 9:22 AM, Martin Morgan
> wrote:

On 01/05/2017 10:18 AM, Charles Determan wrote:

Not to be pushy but did anyone have any insights with this?
I would hate
to have my package still sitting with the bug fix it requires.


maybe svn credentials,

 git svn rebase --username=c.determan

??


Thanks,
Charles

On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan
>
wrote:

Hi,

I received a notification that my package was failing
some tests.  I have
since made the necessary fixes and pushed my changes to
the github repo.
Previously this would result in http://gitsvn.bioconductor.
org/git-push-hook updating the package for
bioconductor.  I noticed
however that this delivery fails and that the git-svn
bridge is no longer
available.

How should I modify my current repository to update my
package
accordingly?

I have my local changes in the 'devel' branch.
I ran the update_ remotes.sh
I run 'git svn rebase' but I get the following error:

Can't create session: Unable to connect to a repository
at URL '

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR

':
Unexpected server error 500 'Internal Server Error' on
'/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
/mingw64/share/perl5/site_perl/Git/SVN.pm line 717.

What did I miss here?
Thanks,

Charles


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Re: [Bioc-devel] update mzR to reflect new Rcpp (RE: https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue)

2017-01-05 Thread Laurent Gatto 

Dear Aaron,

I have just pushed a new version to Bioc svn which will trigger a new
build and a new binary linked against Rcpp 0.12.8, which will get rid of
the warning.

This should however not influence results in any way. If you observe
differences between different versions of xcms, it would be helpful to
report these versions.

Best wishes,

Laurent

On  5 January 2017 16:40, Dickey, Aaron wrote:

> Howdy,
>
> I would like a bump to the mzR package per this issue. I don't
> currently have an error message... but I do have warnings (below) when
> running packages with mzR and Rcpp as dependencies. Also, I would like
> to check that data solutions remain constant. I obtained very
> different results with older versions of bioconductor packages (xcms)
> dependent on these and am trying to troubleshoot.
>
> Warning message:
> In fun(libname, pkgname) :
>   mzR has been built against a different Rcpp version (0.12.7)
> than is installed on your system (0.12.8). This might lead to errors
> when loading mzR. If you encounter such issues, please send a report,
> including the output of sessionInfo() to the Bioc support forum at
> https://support.bioconductor.org/. For details see also
> https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
>
> Thanks.
>
> Aaron M. Dickey, Ph.D.
> Biologist
> U.S. Meat Animal Research Center
> 844 Rd 313, Clay Center, NE 68933
> Phone: (402) 762-4392
> E-mail: aaron.dic...@ars.usda.gov
>
>
>
>
>
> This electronic message contains information generated by the USDA solely for 
> the intended recipients. Any unauthorized interception of this message or the 
> use or disclosure of the information it contains may violate the law and 
> subject the violator to civil or criminal penalties. If you believe you have 
> received this message in error, please notify the sender and delete the email 
> immediately.
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[Bioc-devel] update mzR to reflect new Rcpp (RE: https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue)

2017-01-05 Thread Dickey, Aaron 
Howdy,

I would like a bump to the mzR package per this issue. I don't currently have 
an error message... but I do have warnings (below) when running packages with 
mzR and Rcpp as dependencies. Also, I would like to check that data solutions 
remain constant. I obtained very different results with older versions of 
bioconductor packages (xcms) dependent on these and am trying to troubleshoot.

Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.7)
than is installed on your system (0.12.8). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

Thanks.

Aaron M. Dickey, Ph.D.
Biologist
U.S. Meat Animal Research Center
844 Rd 313, Clay Center, NE 68933
Phone: (402) 762-4392
E-mail: aaron.dic...@ars.usda.gov





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immediately.

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Re: [Bioc-devel] R version-dependent segfault

2017-01-05 Thread Vladimir Kiselev 
Dear Martin,

Many thanks for your reply, it was really helpful. My collaborator ran the
commands you suggested and got the following output:

*
$ Rscript norm_laplacian.R
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
 'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
 -I/home/jake/miniconda3/include
 -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
-I"/home/jake/Documents"   -fpic  -I/home/jake/miniconda3/include  -c
norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/jake/miniconda3/lib/R/lib -L/home/jake/miniconda3/lib
-lgfortran -o sourceCpp_2.so norm_laplacian.o
-L/home/jake/miniconda3/lib/R/lib -lRlapack
-L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
-L/home/jake/miniconda3/lib/R/lib -lR
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10

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] stats graphics  grDevices utils datasets  base

other attached packages:
[1] Rcpp_0.12.8

loaded via a namespace (and not attached):
[1] tools_3.3.2   RcppArmadillo_0.7.600.1.0

$ g++ --version|head -n1
g++ (Ubuntu 6.2.0-5ubuntu12) 6.2.0 20161005
*

So running the simplified code did not produce a segfault and suggested
that the problem was in SC3::norm_laplacian(). And indeed, running valgrind
with SC3::norm_laplacian(matrix(runif(100), nrow = 10)) did catch the error:

*
$ R -d valgrind -f norm_laplacian.R
==7046== Memcheck, a memory error detector
==7046== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==7046== Using Valgrind-3.12.0.SVN and LibVEX; rerun with -h for copyright
info
==7046== Command: /home/jake/miniconda3/lib/R/bin/exec/R -f norm_laplacian.R
==7046==

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> library(Rcpp)
> sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
 'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/include -DNDEBUG
 -I/home/jake/miniconda3/include
 -I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include"
-I"/home/jake/R/x86_64-pc-linux-gnu-library/3.3/RcppArmadillo/include"
-I"/home/jake/Documents"   -fpic  -I/home/jake/miniconda3/include  -c
norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/jake/miniconda3/lib/R/lib -L/home/jake/miniconda3/lib
-lgfortran -o sourceCpp_2.so norm_laplacian.o
-L/home/jake/miniconda3/lib/R/lib -lRlapack
-L/home/jake/miniconda3/lib/R/lib -lRblas -lgfortran -lm -lquadmath
-L/home/jake/miniconda3/lib/R/lib -lR
> xx <- norm_laplacian(matrix(runif(100), nrow = 10))
> SC3::norm_laplacian(matrix(runif(100), nrow = 10))
==7046== Use of uninitialised value of size 8
==7046==at 0x213645B8: direct_max (op_max_meat.hpp:362)
==7046==by 0x213645B8: max (Mat_meat.hpp:6801)
==7046==by 0x213645B8: norm_laplacian(arma::Mat)
(cppFunctions.cpp:87)
==7046==by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)
==7046==by 0x521DE81: R_doDotCall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x522BD99: do_dotcall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267AAC: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526B0A7: do_begin (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526789E: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5268B8C: Rf_applyClosure (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267BBF: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A6C1E: Rf_ReplIteration (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A6DD1: R_ReplConsole (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x52A8758: run_Rmainloop (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==
==7046== Invalid read of size 8
==7046==at 0x213645B8: direct_max (op_max_meat.hpp:362)
==7046==by 0x213645B8: max (Mat_meat.hpp:6801)
==7046==by 0x213645B8: norm_laplacian(arma::Mat)
(cppFunctions.cpp:87)
==7046==by 0x21360E8C: SC3_norm_laplacian (RcppExports.cpp:49)
==7046==by 0x521DE81: R_doDotCall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x522BD99: do_dotcall (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5267AAC: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526B0A7: do_begin (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x526789E: Rf_eval (in
/home/jake/miniconda3/lib/R/lib/libR.so)
==7046==by 0x5268B8C: Rf_applyClosure (in

Re: [Bioc-devel] Updating package

2017-01-05 Thread Charles Determan 
That seems to have been the issue.  It had been some time since I needed to
commit to bioconductor I forgot my username was different.  Thank you
Martin for pointing that simple problem out.  I have now 'dcommit' my
'devel' branch so if I understand correctly the changes should be with
bioconductor to apply accordingly.

Regards,
Charles

On Thu, Jan 5, 2017 at 9:22 AM, Martin Morgan  wrote:

> On 01/05/2017 10:18 AM, Charles Determan wrote:
>
>> Not to be pushy but did anyone have any insights with this?  I would hate
>> to have my package still sitting with the bug fix it requires.
>>
>
> maybe svn credentials,
>
>  git svn rebase --username=c.determan
>
> ??
>
>
>> Thanks,
>> Charles
>>
>> On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan 
>> wrote:
>>
>> Hi,
>>>
>>> I received a notification that my package was failing some tests.  I have
>>> since made the necessary fixes and pushed my changes to the github repo.
>>> Previously this would result in http://gitsvn.bioconductor.
>>> org/git-push-hook updating the package for bioconductor.  I noticed
>>> however that this delivery fails and that the git-svn bridge is no longer
>>> available.
>>>
>>> How should I modify my current repository to update my package
>>> accordingly?
>>>
>>> I have my local changes in the 'devel' branch.
>>> I ran the update_ remotes.sh
>>> I run 'git svn rebase' but I get the following error:
>>>
>>> Can't create session: Unable to connect to a repository at URL '
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR
>>> ':
>>> Unexpected server error 500 'Internal Server Error' on
>>> '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
>>> /mingw64/share/perl5/site_perl/Git/SVN.pm line 717.
>>>
>>> What did I miss here?
>>> Thanks,
>>>
>>> Charles
>>>
>>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>>
>>
>
> 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,
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Re: [Bioc-devel] Updating package

2017-01-05 Thread Martin Morgan 

On 01/05/2017 10:18 AM, Charles Determan wrote:

Not to be pushy but did anyone have any insights with this?  I would hate
to have my package still sitting with the bug fix it requires.


maybe svn credentials,

 git svn rebase --username=c.determan

??



Thanks,
Charles

On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan 
wrote:


Hi,

I received a notification that my package was failing some tests.  I have
since made the necessary fixes and pushed my changes to the github repo.
Previously this would result in http://gitsvn.bioconductor.
org/git-push-hook updating the package for bioconductor.  I noticed
however that this delivery fails and that the git-svn bridge is no longer
available.

How should I modify my current repository to update my package
accordingly?

I have my local changes in the 'devel' branch.
I ran the update_ remotes.sh
I run 'git svn rebase' but I get the following error:

Can't create session: Unable to connect to a repository at URL '
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR':
Unexpected server error 500 'Internal Server Error' on
'/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
/mingw64/share/perl5/site_perl/Git/SVN.pm line 717.

What did I miss here?
Thanks,

Charles



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Re: [Bioc-devel] Updating package

2017-01-05 Thread Charles Determan 
Not to be pushy but did anyone have any insights with this?  I would hate
to have my package still sitting with the bug fix it requires.

Thanks,
Charles

On Wed, Jan 4, 2017 at 11:15 AM, Charles Determan 
wrote:

> Hi,
>
> I received a notification that my package was failing some tests.  I have
> since made the necessary fixes and pushed my changes to the github repo.
> Previously this would result in http://gitsvn.bioconductor.
> org/git-push-hook updating the package for bioconductor.  I noticed
> however that this delivery fails and that the git-svn bridge is no longer
> available.
>
> How should I modify my current repository to update my package
> accordingly?
>
> I have my local changes in the 'devel' branch.
> I ran the update_ remotes.sh
> I run 'git svn rebase' but I get the following error:
>
> Can't create session: Unable to connect to a repository at URL '
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR':
> Unexpected server error 500 'Internal Server Error' on
> '/bioconductor/trunk/madman/Rpacks/OmicsMarkeR' at
> /mingw64/share/perl5/site_perl/Git/SVN.pm line 717.
>
> What did I miss here?
> Thanks,
>
> Charles
>

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Re: [Bioc-devel] R version-dependent segfault

2017-01-05 Thread Martin Morgan 

On 01/05/2017 06:41 AM, Vladimir Kiselev wrote:

My package (SC3 - http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
has a function that causes R version/platform-dependent seqfault. Here is
the function (it's in C++ using RccpArmadillo):

arma::mat norm_laplacian(arma::mat A) {
A = exp(-A/A.max());
arma::rowvec D_row = pow(sum(A), -0.5);
A.each_row() %= D_row;
colvec D_col = conv_to< colvec >::from(D_row);
A.each_col() %= D_col;
arma::mat res = eye(A.n_cols, A.n_cols) - A;
return(res);
}

The test code that provides a segfault on some R versions/platforms:
SC3::norm_laplacian(matrix(runif(100), nrow = 10))


The first line of attack is to simplify the problem as much as possible. 
I did this by writing a C++ file norm_laplacian.cpp


#include 

using namespace arma;

// [[Rcpp::depends(RcppArmadillo)]]

// [[Rcpp::export]]
arma::mat norm_laplacian(arma::mat A) {
A = exp(-A/A.max());
arma::rowvec D_row = pow(sum(A), -0.5);
A.each_row() %= D_row;
colvec D_col = conv_to< colvec >::from(D_row);
A.each_col() %= D_col;
arma::mat res = eye(A.n_cols, A.n_cols) - A;
return(res);
}

and then in R, e.g., norm_laplacian.R

library(Rcpp)
sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
xx <- norm_laplacian(matrix(runif(100), nrow = 10))
sessionInfo()

It would be helpful to use set.seed() to make the example more 
reproducible. One would hope that


R -f norm_laplacian.R

would produce a segfault. Unfortunately not for me. My next step was to 
run this code under valgrind to look for invalid memory access


R -d valgrind -f norm_laplacian.R

again hoping for a report of 'invalid write' or 'invalid read', but 
again no luck for me.


You could see if your collaborators are able to generate segfaults with 
this simpler code. If R -f norm_laplacian.R is sufficient, the next step 
would be to run it under a C-level debugger like gdb, with some hints at 
http://bioconductor.org/developers/how-to/c-debugging/


Here's my output; it's also useful to know information about the 
compiler, and to pay attention to the compiler options (especially 
optimization level -O0 for me)


$ g++ --version|head -n1
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609

$ R --vanilla -f norm_laplacian.R
> library(Rcpp)
> sourceCpp("norm_laplacian.cpp", showOutput=TRUE)
/home/mtmorgan/bin/R-devel/bin/R CMD SHLIB -o 'sourceCpp_2.so' 
'norm_laplacian.cpp'
g++  -I/home/mtmorgan/bin/R-devel/include -DNDEBUG  -I/usr/local/include 

-I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/Rcpp/include" 
-I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5/RcppArmadillo/include" 
-I"/tmp"   -fpic  -g -O0 -c norm_laplacian.cpp -o norm_laplacian.o
g++ -shared -L/home/mtmorgan/bin/R-devel/lib -L/usr/local/lib -o 
sourceCpp_2.so norm_laplacian.o -L/home/mtmorgan/bin/R-devel/lib 
-lRlapack -L/home/mtmorgan/bin/R-devel/lib -lRblas -lgfortran -lm 
-lquadmath -L/home/mtmorgan/bin/R-devel/lib -lR

> xx <- norm_laplacian(matrix(runif(100), nrow = 10))
> sessionInfo()
R Under development (unstable) (2016-12-20 r71827)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 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] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] Rcpp_0.12.8.3

loaded via a namespace (and not attached):
[1] compiler_3.4.0tools_3.4.0
[3] RcppArmadillo_0.7.600.1.0
>


if the segfault does not occur with the simpler code, then one could try 
gdb / valgrind with SC3::norm_laplacian(matrix(runif(100), nrow = 10))


Martin



The segfault usually looks like this:
*** caught segfault ***
address 0x7ffdc981e000, cause 'memory not mapped'

(where address can be a different sequence)

So far by a collaborative effort (me and some users of the package) we
figured out configurations that cause or do not cause a segfault:

* Configurations causing a segfault:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10

* Configurations causing no segfault:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

R Under development (unstable) (2016-10-20 r71540)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

More details on our discussion can be found here:

Re: [Bioc-devel] Which platform are the vignettes built on?

2017-01-05 Thread Vladimir Kiselev 
Great, many thanks Martin!

On Thu, Jan 5, 2017 at 11:22 AM Martin Morgan 
wrote:

> On 01/05/2017 06:16 AM, Vladimir Kiselev wrote:
> > Dear All,
> >
> > After pushing a new version of a package to bioc-devel the vignettes are
> > rebuilt, but I cannot find on which platform they were built on. Is it
> > linux, windows or mac?
>
> They are built on all platforms as part of the build / check cycle. The
> vignettes made available on the web site are from the linux builds.
>
> Martin
>
> >
> > Thanks,
> > Vladimir
> >
>
>
> 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.
>
-- 
http://genat.uk

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[Bioc-devel] R version-dependent segfault

2017-01-05 Thread Vladimir Kiselev 
My package (SC3 - http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
has a function that causes R version/platform-dependent seqfault. Here is
the function (it's in C++ using RccpArmadillo):

arma::mat norm_laplacian(arma::mat A) {
A = exp(-A/A.max());
arma::rowvec D_row = pow(sum(A), -0.5);
A.each_row() %= D_row;
colvec D_col = conv_to< colvec >::from(D_row);
A.each_col() %= D_col;
arma::mat res = eye(A.n_cols, A.n_cols) - A;
return(res);
}

The test code that provides a segfault on some R versions/platforms:
SC3::norm_laplacian(matrix(runif(100), nrow = 10))

The segfault usually looks like this:
*** caught segfault ***
address 0x7ffdc981e000, cause 'memory not mapped'

(where address can be a different sequence)

So far by a collaborative effort (me and some users of the package) we
figured out configurations that cause or do not cause a segfault:

* Configurations causing a segfault:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.10

* Configurations causing no segfault:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

R Under development (unstable) (2016-10-20 r71540)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

More details on our discussion can be found here:
https://github.com/hemberg-lab/SC3/issues/33

Has anybody had a similar issue? Do you have any suggestions on how to fix
this, except rewriting the function in R? Or maybe there already exists a
normalised Laplacian function written in C++?

Many thanks,
Cheers,
Vladimir
-- 
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Re: [Rd] seq.int/seq.default

2017-01-05 Thread Martin Maechler 
> Mick Jordan 
> on Wed, 4 Jan 2017 12:49:41 -0800 writes:

> On 1/4/17 8:15 AM, Mick Jordan wrote:
> Here is another difference that I am guessing is unintended.

>> y <- seq.int(1L, 3L, length.out=2)
>> typeof(y)
> [1] "double"
>> x <- seq.default(1L, 3L, length.out=2)
>> typeof(x)
> [1] "integer"

> The if (by == R_MissingArg) branch at line 842 doesn't contain a check 
> for "all INTSXP" unlike the if (to == R_MissingArg) branch.

> Mick

I'll look at this case, too,
thank you once more!

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Re: [Rd] seq.int/seq.default

2017-01-05 Thread Martin Maechler 
> Mick Jordan 
> on Wed, 4 Jan 2017 08:15:03 -0800 writes:

> On 1/4/17 1:26 AM, Martin Maechler wrote:
>>> Mick Jordan 
>>> on Tue, 3 Jan 2017 07:57:15 -0800 writes:
>> > This is a message for someone familiar with the implementation.
>> > Superficially the R code for seq.default and the C code for seq.int
>> > appear to be semantically very similar. My question is whether, in 
fact,
>> > it is intended that behave identically for all inputs.
>> 
>> Strictly speaking, "no":  As usual, RT?Manual (;-)
>> 
>> The help page says in the very first paragraph ('Description'):
>> 
>> ‘seq’ is a standard generic with a default method.
>> ‘seq.int’ is a primitive which can be much faster but has a few 
restrictions.
>> 
>> > I have found two cases so far where they differ, first
>> > that seq.int will coerce a character string to a real (via
>> > Rf_asReal) whereas seq.default appears to coerce it to NA
>> > and then throws an error:
>> 
>> >> seq.default("2", "5")
>> > Error in seq.default("2", "5") : 'from' cannot be NA, NaN or infinite
>> >> seq.int("2", "5")
>> > [1] 2 3 4 5
>> >>
>> 
>> this may be a bit surprising (if one does _not_ look at the code),
>> indeed, notably because seq.int() is mentioned to have more
>> restrictions than seq() which here calls seq.default().
>> "Surprising" also when considering
>> 
>> > "2":"5"
>> [1] 2 3 4 5
>> 
>> and the documentation of ':' claims 'from:to' to be the same as
>> rep(from,to)  apart from the case of factors.
>> 
>> --- I am considering a small change in  seq.default()
>> which would make it work for this case, compatibly with ":" and 
seq.int().
>> 
>> 
>> > and second, that the error messages for non-numeric arguments differ:
>> 
>> which I find fine... if the functions where meant to be
>> identical, we (the R developers) would be silly to have both,
>> notably as the ".int" suffix  has emerged as confusing the
>> majority of useRs (who don't read help pages).
>> 
>> Rather it has been meant as saying "internal" (including "fast") also 
for other
>> such R functions, but the suffix of course is a potential clash
>> with S3 method naming schemes _and_ the fact that 'int' is used
>> as type name for integer in other languages, notably C.
>> 
>> > seq.default(to=quote(b), by=2)
>> > Error in is.finite(to) : default method not implemented for type 
'symbol'
>> 
>> which I find a very appropriate and helpful message
>> 
>> > seq.int(to=quote(b), by=2)
>> > Error in seq.int(to = quote(b), by = 2) :
>> > 'to' cannot be NA, NaN or infinite
>> 
>> which is true, as well, and there's no "default method" to be
>> mentioned, but you are right that it would be nicer if the
>> message mentioned 'symbol' as well.

> Thanks for the clarifications. It was surprising that seq.int supported 
> more types than seq.default. I was expecting the reverse.

exactly, me too!

> BTW, There are a couple of, admittedly odd, cases, exposed by brute 
> force testing, where seq.int will actually return "missing", which I 
> presume is not intended, and seq.default behaves differently, vis:

>> seq.default(to=1,by=2)
> [1] 1
>> seq.int(to=1,by=2)

>> > x <- seq.int(to=1,by=2)
>> x
> Error: argument "x" is missing, with no default

> Lines 792 and 799 of seq.c return the incoming argument (as opposed to a 
> value based on its coercion to double via asReal) and this can, as in 
> the above example, be "missing".

> Thanks
> Mick Jordan

Thanks a lot, Mick -- you are right!

I'm fixing these  (the line numbers have greatly changed in the
mean time: Remember we work with "R-devel", i.e., the "trunk" :
always available at
https://svn.r-project.org/R/trunk/src/main/seq.c

Martin Maechler
ETH Zurich

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Re: [Bioc-devel] Which platform are the vignettes built on?

2017-01-05 Thread Martin Morgan 

On 01/05/2017 06:16 AM, Vladimir Kiselev wrote:

Dear All,

After pushing a new version of a package to bioc-devel the vignettes are
rebuilt, but I cannot find on which platform they were built on. Is it
linux, windows or mac?


They are built on all platforms as part of the build / check cycle. The 
vignettes made available on the web site are from the linux builds.


Martin



Thanks,
Vladimir




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[Bioc-devel] Which platform are the vignettes built on?

2017-01-05 Thread Vladimir Kiselev 
Dear All,

After pushing a new version of a package to bioc-devel the vignettes are
rebuilt, but I cannot find on which platform they were built on. Is it
linux, windows or mac?

Thanks,
Vladimir
-- 
http://genat.uk

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Re: [Bioc-devel] TabixFileList() constructor broken in devel

2017-01-05 Thread Robert Castelo 

On 05/01/2017 01:37, Martin Morgan wrote:

On 12/29/2016 12:25 PM, Vincent Carey wrote:

A while ago Martin and I discussed the possibility of idempotence for
TabixFile ... this seemed
to make sense and so


TabixFile


function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize =
NA_integer_)

{

if (is(file, "TabixFile"))

return(file)

tryCatch({

.io_check_exists(c(file, index))

}, error = function(err) {

stop(sprintf("TabixFile: %s", conditionMessage(err)),

call. = FALSE)

})

.RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize,

...)

}




TabixFileList could behave similarly, working either from character 
paths,

or from

a list of TabixFile instances, or from a TabixFileList ... might be a
design practice to

promote for S4 programming



TabixFileList


function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize =
NA_integer_)

{

index <- as.character(index)

.RsamtoolsFileList(file, index, ..., yieldSize = yieldSize,

class = "TabixFile")

}



On Thu, Dec 29, 2016 at 11:55 AM, Robert Castelo 


wrote:


hi Lori,

thanks for the clarification. if this is an intended change then i'd 
say

the documentation needs to be updated since, as i showed in my email
below, it currently says that for functions such as 'TabixFileList()'
the input 'file' argument should be a 'TabixFile' instance and not a
character vector.

this change also means the input is switching from a 'TabixFile'
instance to a 'character' vector, so pipelines or packages doing calls
to 'TabixFileList()' that have been passing 'TabixFile' instances as
arguments will have to update those calls to pass a character vector.

  i'd suggest that if there's no good reason to switch, it would be
safer to add the character vector as an additional possibility in the
input argument 'file', just as with 'countTabix()', and minimize
possible breaks of pipelines/packages using 'TabixFileList()'. i've
encountered this problem because my own package VariantFiltering calls
'TabixFileList()' although is not a big deal to fix it.

cheers,

robert.

On 28/12/2016 19:44, Shepherd, Lori wrote:


Thank you for bringing this to our attention. There were some updates
made a few weeks ago to the behavior and input of 'TabixFileList()' .
 Its current implementation will work with a character vector as
input.  I will investigate further into why this change was made and
if it needs to be addressed.


In the meantime:

TabixFileList(tbx)
will throw an ERROR, but you can still use the same file that was used
to create the TabixFile
tbx <- open(TabixFile(fl, yieldSize=100))
TabixFileList(fl)


The original behavior has been restored; both TabixFile() and 
TabixFileList() are idempotent. Sorry for introducing the bug.


Martin


great! thanks Martin!!

robert.




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

 


*From:* Bioc-devel  on behalf of
Robert Castelo 
*Sent:* Wednesday, December 28, 2016 11:50:58 AM
*To:* bioc-devel@r-project.org
*Subject:* [Bioc-devel] TabixFileList() constructor broken in devel
hi,

the 'TabixFileList()' constructor in Rsamtools seems to be broken in
devel:

library(Rsamtools)
example(TabixFileList) ## which actually does not construct any
'TabixFileList'
TabixFileList(tbx)
Error in as.vector(x, "character") :
   cannot coerce type 'environment' to vector of type 'character'

while in release this works fine:

library(Rsamtools)
example(TabixFileList) ## which actually does not construct any
'TabixFileList'
TabixFileList(tbx)
TabixFileList of length 1
names(1): example.gtf.gz

the man page has not changed between devel and release and the current
description of the argument 'file' supports the use of a 'TabixFile'
instance as input:

 file: For TabixFile(), A character(1) vector to the tabix file
   path; can be remote (http://, ftp://). For ‘countTabix’, a
   character(1) or ‘TabixFile’ instance. For others, a
   ‘TabixFile’ instance.

please find below my session information for the devel run.

thanks!

robert.

sessionInfo()
R Under development (unstable) (2016-11-17 r71661)
Platform: x86_64-apple-darwin16.1.0 (64-bit)
Running under: macOS Sierra 10.12.2

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] stats4parallel  stats graphics  grDevices utils 
datasets

[8] methods   base

other attached packages:
  [1] Rsamtools_1.27.9  Biostrings_2.43.1 XVector_0.15.0
  [4] GenomicRanges_1.27.17 GenomeInfoDb_1.11.6 IRanges_2.9.14
  [7] S4Vectors_0.13.5  BiocGenerics_0.21.1 setwidth_1.0-4
[10] colorout_1.1-0

loaded via a namespace (and not attached):
[1]