Re: [Bioc-devel] fatal error when installing BioC devel on R devel
Dear Dan, Thanks for your reply. Unfortunately, the errors remain the same: source(http://bioconductor.org/biocLite.R;) Warning in install.packages : package 'BiocInstaller' is not available (for R Under development) Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2' (as 'lib' is unspecified) Warning in install.packages : cannot open: HTTP status was '403 Forbidden' Warning in install.packages : cannot open: HTTP status was '403 Forbidden' Warning in install.packages : unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 package 'BiocInstaller' is available as a source package but not as a binary Warning in install.packages : package 'BiocInstaller' is not available (for R Under development) 'biocLite.R' failed to install 'BiocInstaller', use 'install.packages(BiocInstaller, repos=http://www.bioconductor.org/packages/2.14/bioc;)' biocLite() Error: could not find function biocLite Should I switch to R 3.1 for beta testing as Martin suggested? BW, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaars...@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Thu, Mar 13, 2014 at 6:13 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Martin Rijlaarsdam m.a.rijlaars...@gmail.com To: bioc-devel bioc-devel@r-project.org Sent: Thursday, March 13, 2014 1:52:20 AM Subject: [Bioc-devel] fatal error when installing BioC devel on R devel Dear Sirs, When trying to install the devel version of Bioconductor on a clean install of R devel I got the following errors: *source(http://bioconductor.org/biocLite.R http://bioconductor.org/biocLite.R)* *Warning in install.packages :* * package 'BiocInstaller' is not available (for R Under development)* *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'* *(as 'lib' is unspecified)* *Warning in install.packages :* * cannot open: HTTP status was '404 Not Found'* *Warning in install.packages :* * cannot open: HTTP status was '404 Not Found'* *Warning in install.packages :* * unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 * * package 'BiocInstaller' is available as a source package but not as a binary* *Warning in install.packages :* * package 'BiocInstaller' is not available (for R Under development)* *'biocLite.R' failed to install 'BiocInstaller', use 'install.packages(BiocInstaller,* * repos=http://www.bioconductor.org/packages/2.14/bioc http://www.bioconductor.org/packages/2.14/bioc)'* Next, I tried: *install.packages(BiocInstaller,repos= http://www.bioconductor.org/packages/2.14/bioc http://www.bioconductor.org/packages/2.14/bioc, type=source)* *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'* *(as 'lib' is unspecified)* *trying URL ' http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz '* *Content type 'application/x-gzip' length 14183 bytes (13 Kb)* *opened URL* *downloaded 13 Kb* ** installing *source* package 'BiocInstaller' ...* *** R* *** inst* *** preparing package for lazy loading* *** help* installing help indices* *** building package indices* *** testing if installed package can be loaded* arch - i386* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* arch - x64* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* ** DONE (BiocInstaller)* *The downloaded source packages are in* * 'C:\Users\lepo\AppData\Local\Temp\RtmpoRLBWv\downloaded_packages'* I then tried to install the default packages and the Gviz package: *source(http://bioconductor.org/biocLite.R http://bioconductor.org/biocLite.R)* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* *biocLite()* *Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/2.14/bioc http://bioconductor.org/packages/2.14/bioc* *biocLite(Gviz)* *Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/2.14/bioc http://bioconductor.org/packages/2.14/bioc* Am I doing something fundamentally wrong here? Or is it a Bioconductor issue? I am using Windows 7 64 bits and have no firewall enabled. Several other (non-devel) versions of R and
Re: [Bioc-devel] fatal error when installing BioC devel on R devel
- Original Message - From: Martin Rijlaarsdam m.a.rijlaars...@gmail.com To: Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel bioc-devel@r-project.org Sent: Friday, March 14, 2014 12:23:36 AM Subject: Re: [Bioc-devel] fatal error when installing BioC devel on R devel Dear Dan, Thanks for your reply. Unfortunately, the errors remain the same: source( http://bioconductor.org/biocLite.R ) Warning in install.packages : package ‘BiocInstaller’ is not available (for R Under development) Installing package into ‘C:/Users/lepo/Documents/R/win-library/3.2’ (as ‘lib’ is unspecified) Warning in install.packages : cannot open: HTTP status was '403 Forbidden' Warning in install.packages : cannot open: HTTP status was '403 Forbidden' Warning in install.packages : unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 package ‘BiocInstaller’ is available as a source package but not as a binary Warning in install.packages : package ‘BiocInstaller’ is not available (for R Under development) 'biocLite.R' failed to install 'BiocInstaller', use 'install.packages(BiocInstaller, repos= http://www.bioconductor.org/packages/2.14/bioc )' biocLite() Error: could not find function biocLite Should I switch to R 3.1 for beta testing as Martin suggested? You should, but unfortunately a binary of R-3.1.0 alpha for windows does not seem to be available on CRAN yet. biocLite() should work for you again in about 10 minutes. Dan BW, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaars...@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Thu, Mar 13, 2014 at 6:13 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Martin Rijlaarsdam m.a.rijlaars...@gmail.com To: bioc-devel bioc-devel@r-project.org Sent: Thursday, March 13, 2014 1:52:20 AM Subject: [Bioc-devel] fatal error when installing BioC devel on R devel Dear Sirs, When trying to install the devel version of Bioconductor on a clean install of R devel I got the following errors: *source( http://bioconductor.org/biocLite.R http://bioconductor.org/biocLite.R )* *Warning in install.packages :* * package 'BiocInstaller' is not available (for R Under development)* *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'* *(as 'lib' is unspecified)* *Warning in install.packages :* * cannot open: HTTP status was '404 Not Found'* *Warning in install.packages :* * cannot open: HTTP status was '404 Not Found'* *Warning in install.packages :* * unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.2 * * package 'BiocInstaller' is available as a source package but not as a binary* *Warning in install.packages :* * package 'BiocInstaller' is not available (for R Under development)* *'biocLite.R' failed to install 'BiocInstaller', use 'install.packages(BiocInstaller,* * repos= http://www.bioconductor.org/packages/2.14/bioc http://www.bioconductor.org/packages/2.14/bioc )'* Next, I tried: *install.packages(BiocInstaller,repos= http://www.bioconductor.org/packages/2.14/bioc http://www.bioconductor.org/packages/2.14/bioc , type=source)* *Installing package into 'C:/Users/lepo/Documents/R/win-library/3.2'* *(as 'lib' is unspecified)* *trying URL ' http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz '* *Content type 'application/x-gzip' length 14183 bytes (13 Kb)* *opened URL* *downloaded 13 Kb* ** installing *source* package 'BiocInstaller' ...* *** R* *** inst* *** preparing package for lazy loading* *** help* installing help indices* *** building package indices* *** testing if installed package can be loaded* arch - i386* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* arch - x64* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help* ** DONE (BiocInstaller)* *The downloaded source packages are in* * 'C:\Users\lepo\AppData\Local\Temp\RtmpoRLBWv\downloaded_packages'* I then tried to install the default packages and the Gviz package: *source( http://bioconductor.org/biocLite.R http://bioconductor.org/biocLite.R )* *Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help*
Re: [Rd] R-3.0.3 tar file not on Sources page
On 13 Mar 2014, at 21:08 , Steven McKinney smckin...@bccrc.ca wrote: Checking CRAN today, I see that on the Sources page http://cran.r-project.org/sources.html that R-3.0.2.tar.gz is still there. R-3.0.3.tar.gz is available from the Older releases are available here. hyperlink to http://cran.r-project.org/src/base/ Is this the right place to report this, for an update to the Sources page? It's a CRAN issue, so c...@r-project.org reaches the right people more efficiently. The front page of CRAN has the right information, so I guess that the Sources page got overlooked. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Detect a terminated pipe
Hi Is there a way to detect that the process that corresponds to a pipe has ended? On my system (Ubuntu 13.04), I see p - pipe(true, w); Sys.sleep(1); system(ps -elf | grep true | grep -v grep); isOpen(p) [1] TRUE The true process has long ended (as the filtered ps system call emits no output), still R believes that the pipe p is open. Thanks for your input. Best regards Kirill __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Detect a terminated pipe
On Mar 14, 2014, at 8:09 AM, Kirill Müller kirill.muel...@ivt.baug.ethz.ch wrote: Hi Is there a way to detect that the process that corresponds to a pipe has ended? On my system (Ubuntu 13.04), I see p - pipe(true, w); Sys.sleep(1); system(ps -elf | grep true | grep -v grep); isOpen(p) [1] TRUE The true process has long ended (as the filtered ps system call emits no output), still R believes that the pipe p is open. As far as R is concerned, the connection is open. In addition, pipes exist even without the process - you can close one end of a pipe and it will still exist (that’s what makes pipes useful, actually, because you can choose to close arbitrary combination of the R/W ends). Detecting that the other end of the pipe has closed is generally done by sending/receiving data to/from the end of interest - i.e. reading from a pipe that has closed the write end on the other side will yield 0 bytes read. Writing to a pipe that has closed the read end on the other side will yield SIGPIPE error (note that for text connections you have to call flush() to send the buffer): p=pipe(true,r) readLines(p) character(0) close(p) p=pipe(true,w) writeLines(, p) flush(p) Error in flush.connection(p) : ignoring SIGPIPE signal close(p) Cheers, Simon Thanks for your input. Best regards Kirill __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Detect a terminated pipe
On 03/14/2014 03:54 PM, Simon Urbanek wrote: As far as R is concerned, the connection is open. In addition, pipes exist even without the process - you can close one end of a pipe and it will still exist (that’s what makes pipes useful, actually, because you can choose to close arbitrary combination of the R/W ends). Detecting that the other end of the pipe has closed is generally done by sending/receiving data to/from the end of interest - i.e. reading from a pipe that has closed the write end on the other side will yield 0 bytes read. Writing to a pipe that has closed the read end on the other side will yield SIGPIPE error (note that for text connections you have to call flush() to send the buffer): p=pipe(true,r) readLines(p) character(0) close(p) p=pipe(true,w) writeLines(, p) flush(p) Error in flush.connection(p) : ignoring SIGPIPE signal close(p) Thanks for your reply. I tried this in an R console and received the error, just like you described. Unfortunately, the error is not thrown when trying the same in RStudio. Any ideas? Cheers Kirill __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Detect a terminated pipe
On Mar 14, 2014, at 11:03 AM, Kirill Müller kirill.muel...@ivt.baug.ethz.ch wrote: On 03/14/2014 03:54 PM, Simon Urbanek wrote: As far as R is concerned, the connection is open. In addition, pipes exist even without the process - you can close one end of a pipe and it will still exist (that’s what makes pipes useful, actually, because you can choose to close arbitrary combination of the R/W ends). Detecting that the other end of the pipe has closed is generally done by sending/receiving data to/from the end of interest - i.e. reading from a pipe that has closed the write end on the other side will yield 0 bytes read. Writing to a pipe that has closed the read end on the other side will yield SIGPIPE error (note that for text connections you have to call flush() to send the buffer): p=pipe(true,r) readLines(p) character(0) close(p) p=pipe(true,w) writeLines(, p) flush(p) Error in flush.connection(p) : ignoring SIGPIPE signal close(p) Thanks for your reply. I tried this in an R console and received the error, just like you described. Unfortunately, the error is not thrown when trying the same in RStudio. Any ideas? RStudio is not R, so it’s possible that they catch signals and fail to distinguish their use from R’s eating the signal before R can get it. I would suggest filing a bug report with RStudio. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Problems building package vignette: Sweave requires multiple passes to build document.
Dear R-devel,
Question:
How can I get Sweave to recognize that the \thebibliography section
is already created and generate the vignette pdf with a single pass? Or
is there a way to let R CMD build know that Sweave needs to be run twice?
If (1) is not possible, any suggestions how to auto-generate a
crude generic bibtex .bib file from my existing document?
Background:
I maintain serveral R packages that include package vignettes. The
vignettes include the reference citations inline as\bibitem lines inside
a thebiblilography section. For some reason, this requires running
Sweave twice on the document (the first pass is presumably preformatting
the citation information?) to produce a pdf. This seems to be the source
of problems when included in R's preferred vignette location
(/vignettes/myPackage.Rnw) because the R package builder just runs
Sweave once during the check process, so no pdf is produced and warnings
are generated like
checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette without corresponding PDF/HTML
In the past, it has been possible for me to pre-build the pdf, and
include it in the /inst/doc/ directory. But it seems the upcoming
versions of R may prohibit this.
It appears that it is possible to avoid all this by including a bibtex
.bib file along with the vignette instead of doing the citations inline.
If the .bib files exists, it seems to generate with a single pass. But
reformatting all of the citations for each document into bibtex will be
a huge pain. Including a blank \bibliography{} command above my
\thebibliography environment also allows the document to be build in a
single pass, but generates a warning about duplicate biliography and
writes the section header twice (not surprisingly).
Note: I've cross-posted this question at:
http://stackoverflow.com/questions/22237675/how-to-get-sweave-to-recognize-thebibliography-environment-and-build-r-package
thanks for your help,
best,
-skye
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Re: [Rd] Problems building package vignette: Sweave requires multiple passes to build document.
On 14/03/2014 12:28 PM, Skye Bender-deMoll wrote:
Dear R-devel,
Question:
How can I get Sweave to recognize that the \thebibliography section
is already created and generate the vignette pdf with a single pass? Or
is there a way to let R CMD build know that Sweave needs to be run twice?
I think the problem isn't Sweave: it ignores LaTeX code. The problem
is the following step that converts the .tex output into a .pdf, which
is handled by tools::texi2pdf (which runs tools::texi2dvi). That
function makes an effort to determine how many LaTeX passes are
required, but it appears you are fooling it somehow.
Take a look at the source to tools::texi2dvi, and see if you can spot
what's going wrong in your case. There are a number of different paths
through that code that depend on your particular setup, so we can't do
that. If you don't succeed in this, then post a simplified sample
package and someone else will be able to see if they have the same
problem as you, and perhaps fix it.
Duncan Murdoch
If (1) is not possible, any suggestions how to auto-generate a
crude generic bibtex .bib file from my existing document?
Background:
I maintain serveral R packages that include package vignettes. The
vignettes include the reference citations inline as\bibitem lines inside
a thebiblilography section. For some reason, this requires running
Sweave twice on the document (the first pass is presumably preformatting
the citation information?) to produce a pdf. This seems to be the source
of problems when included in R's preferred vignette location
(/vignettes/myPackage.Rnw) because the R package builder just runs
Sweave once during the check process, so no pdf is produced and warnings
are generated like
checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette without corresponding PDF/HTML
In the past, it has been possible for me to pre-build the pdf, and
include it in the /inst/doc/ directory. But it seems the upcoming
versions of R may prohibit this.
It appears that it is possible to avoid all this by including a bibtex
.bib file along with the vignette instead of doing the citations inline.
If the .bib files exists, it seems to generate with a single pass. But
reformatting all of the citations for each document into bibtex will be
a huge pain. Including a blank \bibliography{} command above my
\thebibliography environment also allows the document to be build in a
single pass, but generates a warning about duplicate biliography and
writes the section header twice (not surprisingly).
Note: I've cross-posted this question at:
http://stackoverflow.com/questions/22237675/how-to-get-sweave-to-recognize-thebibliography-environment-and-build-r-package
thanks for your help,
best,
-skye
__
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[Rd] Conditional jump or move depends on uninitialised value(s)
Hi, I'm using valgrind to check over some C/C++ code for an R library. I'm getting the report (see below), but can't track down the uninitialised value(s). I tried using --track-origins=yes in valgrind which gives: ==28258== Uninitialised value was created by a stack allocation ==28258==at 0xEE33D98: ??? (in /usr/lib64/R/lib/libRlapack.so) I presume the problem is an uninitialised value being used in my code, rather than in libRlapack, but there is a better way of tracking down where it is? Cheers, Jarrod R -d valgrind --tool=memcheck --leak-check=full --track-origins=yes ==28258== Conditional jump or move depends on uninitialised value(s) ==28258==at 0xEE87208: dstemr_ (in /usr/lib64/R/lib/libRlapack.so) ==28258==by 0xEE7F39B: dsyevr_ (in /usr/lib64/R/lib/libRlapack.so) ==28258==by 0x15B23BD9: ??? (in /usr/lib64/R/modules/lapack.so) ==28258==by 0x15B28397: ??? (in /usr/lib64/R/modules/lapack.so) ==28258==by 0x35CA4BFEAC: ??? (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C8A1F: Rf_eval (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4BB310: Rf_applyClosure (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C58F9: ??? (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C8A1F: Rf_eval (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4BB310: Rf_applyClosure (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C8ACC: Rf_eval (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4CAEE7: ??? (in /usr/lib64/R/lib/libR.so) ==28258== Uninitialised value was created by a stack allocation ==28258==at 0xEE33D98: ??? (in /usr/lib64/R/lib/libRlapack.so) -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Conditional jump or move depends on uninitialised value(s)
On 14/03/2014 17:56, Jarrod Hadfield wrote: Hi, I'm using valgrind to check over some C/C++ code for an R library. I'm R package? getting the report (see below), but can't track down the uninitialised value(s). I tried using --track-origins=yes in valgrind which gives: ==28258== Uninitialised value was created by a stack allocation ==28258==at 0xEE33D98: ??? (in /usr/lib64/R/lib/libRlapack.so) I presume the problem is an uninitialised value being used in my code, rather than in libRlapack, but there is a better way of tracking down where it is? You need debug symbols. Maybe available for your unstated platform, or build a version of R with an internal LAPACK. I doubt this is you: 'Writing R Extensions' has 'Note that memory access errors may be seen with LAPACK, BLAS and Java-using packages: some at least of these seem to be intentional, and some are related to passing characters to Fortran.' Also, it is entirely possible that this is a non-current version of LAPACK: quite a few things like this have been plugged recently. For example, Fedora currently has 3.4.2 and 3.5.0 has been out for a lot longer than Fedora 20. Cheers, Jarrod R -d valgrind --tool=memcheck --leak-check=full --track-origins=yes ==28258== Conditional jump or move depends on uninitialised value(s) ==28258==at 0xEE87208: dstemr_ (in /usr/lib64/R/lib/libRlapack.so) ==28258==by 0xEE7F39B: dsyevr_ (in /usr/lib64/R/lib/libRlapack.so) ==28258==by 0x15B23BD9: ??? (in /usr/lib64/R/modules/lapack.so) ==28258==by 0x15B28397: ??? (in /usr/lib64/R/modules/lapack.so) ==28258==by 0x35CA4BFEAC: ??? (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C8A1F: Rf_eval (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4BB310: Rf_applyClosure (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C58F9: ??? (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C8A1F: Rf_eval (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4BB310: Rf_applyClosure (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4C8ACC: Rf_eval (in /usr/lib64/R/lib/libR.so) ==28258==by 0x35CA4CAEE7: ??? (in /usr/lib64/R/lib/libR.so) ==28258== Uninitialised value was created by a stack allocation ==28258==at 0xEE33D98: ??? (in /usr/lib64/R/lib/libRlapack.so) -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
