search for: kasperdanielhansen

>>>>> Kasper Daniel Hansen <kasperdanielhansen at gmail.com> >>>>> on Fri, 19 May 2017 20:09:24 -0400 writes: > I rebuilt R with > export LC_CTYPE=en_US.UTF-8 > and the test still fail. Surprisingly, when I run R from the bin directory > and execute the test code, it runs without error: &gt...

...uestion at midnight, especially when I know it forks the process and it's not using threads. Brain meltdown. (So, we'll proceed trying to use pthreads in matrixStats also for Windows). Sorry for the noise and thanks Kasper. Henrik On Aug 15, 2015 02:52, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com> wrote: > mclapply uses fork which is different from pthreads. As I understand it, > pthreads requires you to rewrite code, fork is a system call which takes > care of completely replicating the current state of the process. > > Kasper > > On Fri, Aug 14, 2015...

On RedHat Enterprise Linux 6, the test below fails (this is using the stock GCC 4.4.7) from R-devel r72707. LC_CTYPE is unset when I run it, but LANG=en_US.UTF-8 It also failed "yesterday" where as far as I recall the test code looked a bit different. Best, Kasper > ## Results differed by platform, but some gave incorrect results on string 10. > > > ## str() on large

Hi, We have several projects in the center done by researchers over years in Fortran, there are copy right issues etc to prevent us from giving away the source codes, but a lot of social scientist are interested to use the program. We tried to use dlls to make plugins (available in our website) in various statistics platforms (SAS, STATA and R) to make it available to general public. We used

...w a bug in? > ? make check > in R-development (tested today with r79361). As I see it, I specify a > reasonable TZ environment variable and this leads to make check emitting > an error. > > Best, > Kasper > > On Fri, Oct 2, 2020 at 11:28 AM Kasper Daniel Hansen > <kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at gmail.com>> wrote: > > Yes, the potential issue I see is that? > ? make check? > fails when I explicitly?set TZ. However, I set it to be the same as > what the system reports when I login. > > Details: Th...

...one I will explain 100% of the variance? I think showing 'Total Proportion of Variance' is important if that is the case. Regards, Steve Bronder Website: stevebronder.com Phone: 412-719-1282 Email: sbronder at stevebronder.com On Thu, Mar 24, 2016 at 2:58 PM, Kasper Daniel Hansen < kasperdanielhansen at gmail.com> wrote: > Martin, I fully agree. This becomes an issue when you have big matrices. > > (Note that there are awesome methods for actually only computing a small > number of PCs (unlike your code which uses svn which gets all of them); > these are available in various...

I am running into a problem with the 00LOCK file and .nfs files. It seemed to be caused by the following R is installed on NFS user A has loaded pkg_A containing a dynamically loaded library user B (the administrator) runs install.packages("pkg_A") as the final part of the installation process the 00LOCK directory is removed this creates a .nfs file because user A has the

Yes, the potential issue I see is that make check fails when I explicitly set TZ. However, I set it to be the same as what the system reports when I login. Details: The system (RHEL) I am working on has $ strings /etc/localtime | tail -n 1 EST5EDT,M3.2.0,M11.1.0 $ date +%Z EDT $ echo $TZ US/Eastern On Fri, Oct 2, 2020 at 9:48 AM Sebastian Meyer <seb.meyer at fau.de> wrote: > Thank

Related to this question: I have installed bzip2 1.0.6 by hand, but configure still fails. When I look at config.log I get the following configure:34150: /usr/bin/gcc -std=gnu99 -o conftest -g -O2 -march=amdfam10 -g -O2 -march=amdfam10 -L/usr/local/lib64 confte st.c -lbz2 -lz -lrt -ldl -lm >&5 conftest.c: In function 'main': conftest.c:250: warning: initialization discards

...nd occurs even in packages that have no dependencies or R code in them. The post below from Henrik points to a possible cause. Thanks, Dan On Fri, Apr 12, 2013 at 4:23 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote: > On Fri, Apr 12, 2013 at 3:53 PM, Kasper Daniel Hansen > <kasperdanielhansen at gmail.com> wrote: >> Dan, >> >> This error looks _very_ similar to what I reported regarding the use of >> 'foreach' inside a windows vignette, on the bioc-devel email list. As you >> say, it looks funny that it lists the tex file, yet fails to find it....

...t if that is the case. >> >> >> Regards, >> >> Steve Bronder >> Website: stevebronder.com >> Phone: 412-719-1282 >> Email: sbronder at stevebronder.com >> >> >> On Thu, Mar 24, 2016 at 2:58 PM, Kasper Daniel Hansen < >> kasperdanielhansen at gmail.com> wrote: >> >>> Martin, I fully agree. This becomes an issue when you have big matrices. >>> >>> (Note that there are awesome methods for actually only computing a small >>> number of PCs (unlike your code which uses svn which gets all of...

...n_US.UTF-8" (? from system("locale -a| fgrep .UTF-8") ) + } > stopifnot(identical(Sys.setlocale("LC_CTYPE", mbyte.lc), mbyte.lc)) > oloc [1] "en_US.UTF-8" > mbyte.lc [1] "en_US.UTF-8" On Fri, May 19, 2017 at 7:29 PM, Kasper Daniel Hansen < kasperdanielhansen at gmail.com> wrote: > On RedHat Enterprise Linux 6, the test below fails (this is using the > stock GCC 4.4.7) from R-devel r72707. LC_CTYPE is unset when I run it, but > LANG=en_US.UTF-8 > > It also failed "yesterday" where as far as I recall the test code looked a &...

When I build a package containing a vignette, the package gets installed to build the vignette. However, it appears that R CMD build does not allow for --configure-args. In my case, I have a C library installed in a non-standard position, and I need to tell the package where it is. It works fine with R CMD INSTALL, but R CMD build complains Warning: unknown option

This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘bumphunter’ Adding so many packages to the search path is excessive and importing selectively is preferable. Let us say my package A either uses a class B (by producing an object that has B embedded as a slot) from another package or provides a

...existing (or even defunct) packages. I would love to see this included as an optional but canonical part of the R package structure, but for now I will simply put it in inst/bib. I humbly suggest other people consider doing the same. ~G On Sun, Nov 17, 2013 at 6:31 PM, Kasper Daniel Hansen < kasperdanielhansen@gmail.com> wrote: > Fellow package authors, > > I have been reviewing a number of Bioconductor packages for a publication, > and for that purpose I have been interested in citing numerous packages. > For (too many) packages it has been (too) hard to find the relevant > inform...

Following from the R-help thread of March 22 on "Memory usage in prcomp", I've started looking into adding an optional 'rank.' argument to prcomp allowing to more efficiently get only a few PCs instead of the full p PCs, say when p = 1000 and you know you only want 5 PCs. (https://stat.ethz.ch/pipermail/r-help/2016-March/437228.html As it was mentioned, we already

...it only installs a shared library if you use a special Makefile (this is clearly stated in the installation docs) and (2) I had to symlink libbz2.so.1 to libbz2.so.1.0.6 (the included libbz2.so.1.0 was not being picked up). Best, Kasper On Fri, Mar 27, 2015 at 11:19 AM, Kasper Daniel Hansen < kasperdanielhansen at gmail.com> wrote: > Related to this question: > > I have installed bzip2 1.0.6 by hand, but configure still fails. When I > look at config.log I get the following > > configure:34150: /usr/bin/gcc -std=gnu99 -o conftest -g -O2 > -march=amdfam10 -g -O2 -march=amdfam10...

On Windows there are a few 'pthreads' implementation, e.g. pthreads-w32 and winpthreads [https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-pthreads]. We're thinking of giving them a try for the matrixStats package, and basic tests indicates it works, but since Windows pthreads are not used by core R (or?) I've got a little bit worried that we will face overwhelming

I am trying to compile R under a new setup, and frankly, I have had a lot of problems, but I think the stuff below points to a possible bug in R's (custom) configure checks for C++11/14/17, but not for C++98. This is a report about R from the R-3-6 branch, with a svn checkout from today, revision r77135. In my case the compiler name is x86_64-conda_cos6-linux-gnu-g++, not g++. I denote this

...I think the issue is.. In my opinion there is now a bug in make check in R-development (tested today with r79361). As I see it, I specify a reasonable TZ environment variable and this leads to make check emitting an error. Best, Kasper On Fri, Oct 2, 2020 at 11:28 AM Kasper Daniel Hansen < kasperdanielhansen at gmail.com> wrote: > Yes, the potential issue I see is that > make check > fails when I explicitly set TZ. However, I set it to be the same as what > the system reports when I login. > > Details: The system (RHEL) I am working on has > $ strings /etc/localtime | tail -n...