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...ed by coercion probably because 'size' was > .Machine$integer.max for one of the files included in the tarball. This suggests that the resulting tarball might be incorrect. Which is confirmed later when running 'tar ztvf' on that tarball from the Unix comand line: -rw-r--r-- biocbuild/phs_compbio 38 2012-12-11 09:37 ChIPXpressData/.BBSoptions -rw-r--r-- biocbuild/phs_compbio 442 2013-01-18 12:04 ChIPXpressData/DESCRIPTION -rw-r--r-- biocbuild/phs_compbio 0 2012-12-11 09:37 ChIPXpressData/NAMESPACE -rw-r--r-- biocbuild/phs_compbio 14 2012-12-11 09:37 ChIPXpressDat...

...The error does not occur with gctorture(TRUE); tools::buildVignettes(dir="DirichletMultinomial"). By setting a breakpoint at Rf_error and creating a back-trace (gdb) bt #0 Rf_error ( format=0x7ffff7a7cef8 "invalid primitive operation given for dispatch") at /home/biocbuild/src/R-3.0.r62077/src/main/errors.c:741 #1 0x00007ffff793a7ed in R_possible_dispatch (call=0x164d5c0, op=0x4d772a0, args=0x53325d0, rho=0x5334428, promisedArgs=TRUE) at /home/biocbuild/src/R-3.0.r62077/src/main/objects.c:1414 #2 0x00007ffff7908463 in Rf_DispatchOrEval (call=0x164d5c0, op...

Hi, Trying to compile one of the latest snapshot tarballs of R-devel gives me the following error (64-bit openSUSE 10.3): ... make[2]: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/R/src/library/Recommended' make[2]: *** No rule to make target `VR.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory `/loc/home/biocbuild/bbs-2.4-bioc/R/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: Lea...

...re is some bug in the byte-compiler that seems to make it treat `&&` like if it were `&` when compiling foo. Cheers, H. > sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS Matrix products: default BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/libRblas.so LAPACK: /home/biocbuild/bbs-3.5-bioc/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C...

...valid uid value replaced by that for user 'nobody' Warning: invalid uid value replaced by that for user 'nobody' Warning: invalid uid value replaced by that for user 'nobody' One thing to note is that I am logged in as 'pkgbuild' and R was installed by the user 'biocbuild'. I explicitly point to the R that was installed by 'biocbuild' when building the package above. (I used the command "~biocbuild/bbs-2.13-bioc/R/bin/R CMD build anRpackage"). There doesn't seem to be anything wrong with the ownership of the files in anRpackage: $ ls -lR...

...ng URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' Content type 'application/zip' length 4287270 bytes (4.1 Mb) opened URL downloaded 4.1 Mb package 'XML' successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\biocbuild\AppData\Local\Temp\3\Rtmps7OWh0\downloaded_packages trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip' Content type 'application/zip' length 4287270 bytes (4.1 Mb) opened URL downloaded 4.1 Mb package 'XML' successfully unpacked and MD5 sums checked...

...9;http://cran.fhcrc.org/bin/windows/contrib/2.5/XML_1.4-0.zip' Content type 'application/zip' length 1647612 bytes opened URL downloaded 1608Kb package 'XML' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\biocbuild\Local Settings\tmpdir\RtmpXybdrb\downloaded_packages updating HTML package descriptions > library(XML) Error in Sys.putenv(names(x), as.character(unlist(x))) : wrong type for argument Error: .onLoad failed in 'loadNamespace' for 'XML' Error: package/namespac...

...;install.packages' source code, it seems that this warning is issued only when 'length(.libPaths()) > 1'. So typically, this warning will appear on Mac OS X but not on a Linux or Windows systems with default settings. On my Mac OS X system: > .libPaths() [1] "/Users/biocbuild/Library/R/Library" [2] "/Library/Frameworks/R.Framework/Versions/2.3/Resources/library" but on my Linux system: > .libPaths() [1] "/home/hpages/arch/x86_64/R-2.3.1/library" I'm using R-2.3.1 on both systems. Best, H. -- ------------------------ He...

Full_Name: Brian K. Boonstra Version: 2.2.1 OS: WinXP, OSX Submission from: (NULL) (63.172.178.137) The maxdrawdown function in tseries defines the maximum drawdown in terms of absolute dollars (or whatever units the input is in). Industry convention is to do this in percentage terms. I have written the code below as maximumdrawdown(), which retains backward compatibility with the current

...n,Chenwei Description: Annotation data file for hgu95av2 assembled using data from public data repositories Maintainer: Lin,Chenwei < clin at fhcrc.org > LazyLoad: yes Depends: R(>= 2.0.0) License: LGPL Packaged: Thu Mar 3 15:43:00 2005; biocbuild It is an example database of the geneplotter library. Trying to install, I got: $ R CMD INSTALL hgu95av2_1.7.0.tar.gz * Installing *source* package 'hgu95av2' ... ** R ** data ** preparing package for lazy loading Error: 'delay' is defunct. Use 'delayedAssign' ins...

...reasons, but it happens. Would it be possible that I() has a less destructive effect on S4 objects? Thanks, H. > sessionInfo() R Under development (unstable) (2020-10-17 r79346) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.1 LTS Matrix products: default BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=...

...esn't give the same thing as foo(c(a=TRUE, b=FALSE)). Duncan Murdoch > > Cheers, > H. > > > sessionInfo() > R version 3.4.0 (2017-04-21) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.2 LTS > > Matrix products: default > BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/libRblas.so > LAPACK: /home/biocbuild/bbs-3.5-bioc/R/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_...

...it > treat `&&` like if it were `&` when compiling foo. > > Cheers, > H. > > > sessionInfo() > R version 3.4.0 (2017-04-21) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.2 LTS > > Matrix products: default > BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/libRblas.so > LAPACK: /home/biocbuild/bbs-3.5-bioc/R/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPE...

...oing, e.g., for 'M' above ? Martin > > Thanks, > H. > > > sessionInfo() > R Under development (unstable) (2020-10-17 r79346) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 20.04.1 LTS > > Matrix products: default > BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so > LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7]...

...sulting .tar.gz file contains ppiData/inst/doc/ppiData.tex Then the package fails check (excerpt of ppiData.Rcheck/00install.out): Error in vignette_type(Outfile) : Vignette product ?ppiData.tex? does not have a known filename extension (?NA?) ERROR: installing vignettes failed * removing ?/home/biocbuild/bbs-2.12-data-experiment/meat/ppiData.Rcheck/ppiData? This package does not have a vignette Makefile either, so I'm not sure why the tex file is included in the .tar.gz. These two errors are with: > sessionInfo() R version 3.0.0 alpha (2013-03-09 r62188) Platform: x86_64-unknown-linux-gnu...

Hi, we noticed that since some time after Aug 24th the daily snapshots provided on ftp://ftp.stat.math.ethz.ch/Software/R/ no longer have their default tarball file name but dropped the date stamp, i.e. R-devel_.tar.bz2 Same for R-patched snapshots. Could one of the maintainers please take a look. We rely on the default naming convention for automatic builds. Regards, Matthias --

Hi, After installing Rtools 3.1.0.1939 into c:\rtools31, when I call any (most?) of the commands in c:\rtools31\bin, I see strange messages printed to stderr. Example: C:\Rtools31>bin\tar 0 [main] tar 6084 shared_info::initialize: size of shared memory region changed from 27984 to 21136 bin/tar: You must specify one of the `-Acdtrux' options Try `bin/tar --help' or `bin/tar

...rface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields. License: GPL-2 URL: http://www.rforge.net/rJava/ SystemRequirements: java Repository: CRAN Date/Publication: 2011-12-11 10:41:33 Packaged: 2012-10-19 17:13:34 UTC; biocbuild Built: R 2.16.0; i386-w64-mingw32; 2012-10-19 17:36:53 UTC; windows

...the build machines to the latest R devel. It's causing some confusion and breaks at least one unit test. Thanks, H. > sessionInfo() R Under development (unstable) (2024-03-06 r86056) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.4 LTS Matrix products: default BLAS:?? /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C ?[3] LC_TIME=en_GB????????????? LC_COLLATE=en_US.UTF-8 ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8 ?[7] LC_PAPER=en_US.UTF-8?????? LC_NA...

...> >> >> Thanks, >> H. >> >> > sessionInfo() >> R Under development (unstable) (2020-10-17 r79346) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Ubuntu 20.04.1 LTS >> >> Matrix products: default >> BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so >> LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAG...