similar to: readLines() for non-blocking pipeline behaves differently in R 3.5

The issue is that readLines() tries to seek (for reasons I don't understand) in the non-blocking case, but silently fails for "stdin" since it's a stream. This confused the buffering logic. The fix is to mark "stdin" as unable to seek, but I do wonder why readLines() is seeking in the first place. Anyway, I'll get this into patched ASAP. Thanks for the report.

I suspect the reason for the seek is this: cat("1\n", file = "foobar") f <- file("foobar", blocking = FALSE, open = "r") readLines(f) #> [1] "1" cat("2\n", file = "foobar", append = TRUE) readLines(f) #> [1] "2" cat("3\n", file = "foobar", append = TRUE) readLines(f) #> [1]

Probably related to the switch to buffered connections. I will look into this soon. On Wed, Apr 25, 2018 at 2:34 PM, Randy Lai <randy.cs.lai at gmail.com> wrote: > It seems that the behavior of readLines() in R 3.5 has changed for non-blocking pipeline. > > > Consider the following R script, which reads from STDIN line by line. > ``` > con <- file("stdin")

Getting this when attempting to build 2.3.11.3 on CentOS 6: test-mail-cache.c:176: Assert failed: strcmp(str_c(str),"123\nfoo\n456\nbar\n") "" != "123 foo 456 bar " test-mail-cache.c:176: Assert failed: strcmp(str_c(str),"123\nfoo\n456\nbar\n") "" != "123 foo 456 bar " mail cache uncommitted lookups

You bet - it's available on github at https://github.com/UW-GAC/wgsaparsr/blob/master/tests/testthat/1k_annotation.gz -Ben On Thu, May 10, 2018 at 4:17 PM, Michael Lawrence <lawrence.michael at gene.com > wrote: > Would it be possible to get that file or a representative subset of it > somewhere so that I can reproduce this? > > Thanks, > Michael > > On Thu, May

When I read a .gz file with readLines() in 3.4.3, it returns text (and a warning). In 3.5.0, it gives a warning, but no text. Is this expected behavior or a bug? 3.4.3: > source_file = "1k_annotation.gz" > readfile_con <- gzfile(source_file, "r") > readLines(readfile_con, n = 5) [1] "#chr\tpos\tref\talt\t <truncated output here> Warning message: In

The issue was reported to me for?https://github.com/randy3k/rtichoke/issues/50 which is a python program which embeds R and provides a interface to R. With R 3.5,?for reason which i don't understand, when I typed `"a"` in the console STDOUT got `"\x02\xff\xfea\x03\xff\xfe"`?with the extra escaped characters. I notice that `\x02\xff\xfe` and `\x03\xff\xfe` are encoding

Would it be possible to get that file or a representative subset of it somewhere so that I can reproduce this? Thanks, Michael On Thu, May 10, 2018 at 3:31 PM, Ben Heavner <bheavner at gmail.com> wrote: > When I read a .gz file with readLines() in 3.4.3, it returns text (and a > warning). In 3.5.0, it gives a warning, but no text. Is this expected > behavior or a bug? > >

I am using Sublime Text as my editor. If I run `subl -n .Rprofile` in bash, a file would be opened in a new window. Back in R, if I run this > file.edit(".Rprofile", editor="'subl -n'") sh: 'subl -n': command not found Warning message: error in running command However, the interesting bit happens when I run edit(1:10, editor="'subl -n?") It

Dear R-help, I think I have kinda isolated the problem I had to the following: i <- 0 while( {i <- i + 1} < 5) { if(i < 3) next print(i) } This seems to go into an infinite loop. After I break the execution, i has the value 1. At the R prompt, if I start from i <- 0 and keep typing {i <- i + 1} < 5, it eventually evaluate to TRUE. So why does the while loop not work?

A line was added to call `R_SetParams ` in the function `R_SetWin32` 4 days ago. https://github.com/wch/r-source/blob/2370eca96267e29a69396ef53a52ff5d6f60c65b/src/gnuwin32/system.c#L780 However, `R_SetParams` actually calls `R_SetWin32`. https://github.com/wch/r-source/blob/30f7698e19fe1d2ce8fe53d85cd6cfad21fc8bb0/src/main/startup.c#L284 So it results in a stack overflow. Related commit by Luke

On 15. Aug 2020, at 14.18, Peter <peter at pajamian.dhs.org> wrote: > > Getting this when attempting to build 2.3.11.3 on CentOS 6: > > test-mail-cache.c:176: Assert failed: strcmp(str_c(str),"123\nfoo\n456\nbar\n") > "" != "123 > foo > 456 > bar > " > test-mail-cache.c:176: Assert failed:

I am interested in testing two similar nls models to determine if the lines are statistically different when fitted with two different data sets; one corn, another soybean. I know I can do this in linear models by testing for interactions. See Introductory Statistics with R by Dallgaard p212-218 for an example. I have two different data sets I am comparing to lai. ci.re should have very

Is there a "canned" function in R for finding the standard error of the mean? I have tried > sem <- function(x) c(mean =mean(x), + SEM = stdev(x)/sqrt(length(x))) > sem(pnet.lai) Error in sem(pnet.lai) : couldn't find function "stdev" It looks like there is no stdev function in R Thanks, Kirk Kirk R. Wythers email: kwythers at umn.edu University of

There was a discussion on r-help of getting the output from print.packageInfo into a file. Spencer and I have added a file= argument to print.packageInfo for consideration in R. Had this been available it would have simplified the answer to that thread. If the file= argument is used then the packageInfo information is sent to the file specified rather than displayed using file.show .

Thanks it worked for me. I wanted to plot days since planting on x-axis 1 and years on x-axis 3. LAI_simulation$Date <- as.Date( LAI_simulation$Date, '%Y/%m/%d') LAI_simulation$Date <- as.integer(LAI_simulation$Date - as.Date("2009-10-07")) plot(LAI~Date,data=LAI_simulation,xlab="Days since Oct, 7,

Compilation failure on c/s 17194 is as follows: /root/randy/vtd-stage/xen/common/built_in.o: In function `guest_remove_page'': /root/randy/vtd-stage/xen/common/memory.c:172: undefined reference to `__bitop_bad_size'' /root/randy/vtd-stage/xen/common/memory.c:172: relocation truncated to fit: R_X86_64_PC32 against undefined symbol `__bitop_bad_size''

Hai? ? Im running:?debian wheezy, sernet samba 4.1.3 , DC, in windows 2008 AD domain. ? Im reading the wiki and i stumbled on this. https://wiki.samba.org/index.php/Dns-backend_bind? semanage fcontext -a -t named_var_run_t /usr/local/samba/private/dns/${MYREALM}.zone semanage fcontext -a -t named_var_run_t /usr/local/samba/private/dns/${MYREALM}.zone.jnl the strange thing is, and this is

Dear all, I have several questions regarding fisher.test() in R, and I'd highly appreciate any help with it. I have a group of observations, each having people's income, and an indicator of whether selected in or out a program. I want to test the difference between income of people who are in and out. Because the distribution is far from normal, I decide to use the fisher's exact

Dear all, I have several questions regarding fisher.test() in R, and I'd highly appreciate any help with it. I have a group of observations, each having people's income, and an indicator of whether selected in or out a program. I want to test the difference between income of people who are in and out. Because the distribution is far from normal, I decide to use the fisher's exact