Hi, R-2.1.1 OS: OpenBSD-current (3.8) on i386 Compiler:gcc version 3.3.5 (propolice) Thread model: single configure \ --with-readline \ --with-tcltk \ --with-tcl-config=/usr/local/lib/tcl8.4/tclConfig.sh \ --with-tk-config=/usr/local/lib/tk8.4/tkConfig.sh \ --with-libpng \ --with-jpeglib \ --with-zlib \ --with-bzlib \ --with-pcre \ --with-libiconv-prefix=/usr/local/ I'm brand new to R so I don't know how critical this error is. Here's the last bit what make check FORCE=FORCE outputs: running code in 'grDevices-Ex.R' ... OK comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.prev' ... OK running code in 'graphics-Ex.R' ... OK comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.prev' ... OK running code in 'stats-Ex.R' ... OK comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.prev' ... OK running code in 'datasets-Ex.R' ... OK comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.prev' ... OK running code in 'methods-Ex.R' ... OK comparing 'methods-Ex.Rout' to 'methods-Ex.Rout.prev' ... OK running code in 'grid-Ex.R' ... OK comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.prev' ... OK running code in 'splines-Ex.R' ... OK comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.prev' ... OK running code in 'stats4-Ex.R' ... OK comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.prev' ... OK running code in 'tcltk-Ex.R' ... OK comparing 'tcltk-Ex.Rout' to 'tcltk-Ex.Rout.prev' ... OK updating test dependencies `Makedeps' is up to date. running strict specific tests running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'primitive-funs.R' ... OK comparing 'primitive-funs.Rout' to './primitive-funs.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ...*** Error code 1 Stop in /usr/local/src/R-2.1.1/tests. *** Error code 1 Stop in /usr/local/src/R-2.1.1/tests (line 206 of Makefile). *** Error code 1 Stop in /usr/local/src/R-2.1.1/tests (line 191 of Makefile). Tried finding this error in the archives to no avail. If it is okay to ignore this error, how can I skip this test? Thanks for any input! Jeff Ross
Make check fails on d-p-q-r-tests.R...
5 messages · Jeff Ross, Brian Ripley
You will have to show us the error! It will be shown in d-p-q-r-tests.Rout.fail (unless this was a segfault or similar). It is not OK to skip the test, but note that this test is random and does fail about 1 in 50 times, so you could just try rerunning it.
On Mon, 26 Sep 2005, Jeff Ross wrote:
Hi, R-2.1.1 OS: OpenBSD-current (3.8) on i386 Compiler:gcc version 3.3.5 (propolice) Thread model: single configure \ --with-readline \ --with-tcltk \ --with-tcl-config=/usr/local/lib/tcl8.4/tclConfig.sh \ --with-tk-config=/usr/local/lib/tk8.4/tkConfig.sh \ --with-libpng \ --with-jpeglib \ --with-zlib \ --with-bzlib \ --with-pcre \ --with-libiconv-prefix=/usr/local/
Please do NOT use unrecommended flags like --with-zlib, especially not on your first build. None of those flags should have been needed.
I'm brand new to R so I don't know how critical this error is. Here's the last bit what make check FORCE=FORCE outputs: running code in 'grDevices-Ex.R' ... OK comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.prev' ... OK running code in 'graphics-Ex.R' ... OK comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.prev' ... OK running code in 'stats-Ex.R' ... OK comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.prev' ... OK running code in 'datasets-Ex.R' ... OK comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.prev' ... OK running code in 'methods-Ex.R' ... OK comparing 'methods-Ex.Rout' to 'methods-Ex.Rout.prev' ... OK running code in 'grid-Ex.R' ... OK comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.prev' ... OK running code in 'splines-Ex.R' ... OK comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.prev' ... OK running code in 'stats4-Ex.R' ... OK comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.prev' ... OK running code in 'tcltk-Ex.R' ... OK comparing 'tcltk-Ex.Rout' to 'tcltk-Ex.Rout.prev' ... OK updating test dependencies `Makedeps' is up to date. running strict specific tests running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'primitive-funs.R' ... OK comparing 'primitive-funs.Rout' to './primitive-funs.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ...*** Error code 1 Stop in /usr/local/src/R-2.1.1/tests. *** Error code 1 Stop in /usr/local/src/R-2.1.1/tests (line 206 of Makefile). *** Error code 1 Stop in /usr/local/src/R-2.1.1/tests (line 191 of Makefile). Tried finding this error in the archives to no avail. If it is okay to ignore this error, how can I skip this test? Thanks for any input! Jeff Ross
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Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595
On 1:03:39 am 09/27/05 Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
You will have to show us the error! It will be shown in d-p-q-r-tests.Rout.fail (unless this was a segfault or similar). It is not OK to skip the test, but note that this test is random and does fail about 1 in 50 times, so you could just try rerunning it.
I am so sorry. I didn't even think to look for a .fail file. Here is the last bit of it:
## for PR#7902:
ex <- -c(rev(1/x), ex) All.eq(-x, qcauchy(pcauchy(-x)))
[1] TRUE
All.eq(+x, qcauchy(pcauchy(+x, log=TRUE), log=TRUE))
[1] TRUE
All.eq(1/x, pcauchy(qcauchy(1/x)))
[1] TRUE
All.eq(ex, pcauchy(qcauchy(ex, log=TRUE), log=TRUE))
[1] "`is.NA' value mismatches: 1 in current, 0 in target" Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p)
II <- c(-Inf,Inf) stopifnot(pcauchy(II) == 0:1, ## qcauchy(0:1) == II,
+ pcauchy(II, log=TRUE) == c(-Inf,0), + qcauchy(c(-Inf,0), log=TRUE) == II) Error in if (!(is.logical(r <- eval(ll[[i]])) && all(r))) stop(paste(deparse(mc[[i + : missing value where TRUE/FALSE needed In addition: Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p) Execution halted This is from the latest R-patched source tar ball, and it is the identical error as R-2.1.1. I've consistently gotten the same error, even with configuration file tweaks and making clean between runs. Thanks! Jeff Ross
I am afraid this does look like a real problem, if a minor one. We have for the first problem x <- 10^(ex <- c(1,2,5*(1:5),50,100,200,300,Inf)) ex <- -c(rev(1/x), ex) qcauchy(ex, log=TRUE) The first entry of the result should be Inf and the last -Inf. From the output you have shown us I would guess the last is NaN. If this is what is going on, it is a problem but a somewhat esoteric one that probably reflects a lack of IEC60559 (aka IEEE754) conformance. It needs more hands-on debugging than we can provide on a help list.
On Tue, 27 Sep 2005, Jeff Ross wrote:
On 1:03:39 am 09/27/05 Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
You will have to show us the error! It will be shown in d-p-q-r-tests.Rout.fail (unless this was a segfault or similar). It is not OK to skip the test, but note that this test is random and does fail about 1 in 50 times, so you could just try rerunning it.
I am so sorry. I didn't even think to look for a .fail file. Here is the last bit of it:
## for PR#7902:
ex <- -c(rev(1/x), ex) All.eq(-x, qcauchy(pcauchy(-x)))
[1] TRUE
All.eq(+x, qcauchy(pcauchy(+x, log=TRUE), log=TRUE))
[1] TRUE
All.eq(1/x, pcauchy(qcauchy(1/x)))
[1] TRUE
All.eq(ex, pcauchy(qcauchy(ex, log=TRUE), log=TRUE))
[1] "`is.NA' value mismatches: 1 in current, 0 in target" Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p)
II <- c(-Inf,Inf) stopifnot(pcauchy(II) == 0:1, ## qcauchy(0:1) == II,
+ pcauchy(II, log=TRUE) == c(-Inf,0), + qcauchy(c(-Inf,0), log=TRUE) == II) Error in if (!(is.logical(r <- eval(ll[[i]])) && all(r))) stop(paste(deparse(mc[[i + : missing value where TRUE/FALSE needed In addition: Warning message: NaNs produced in: qcauchy(p, location, scale, lower.tail, log.p) Execution halted This is from the latest R-patched source tar ball, and it is the identical error as R-2.1.1. I've consistently gotten the same error, even with configuration file tweaks and making clean between runs. Thanks! Jeff Ross
Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595
On Tue, 27 Sep 2005, Prof Brian Ripley wrote:
I am afraid this does look like a real problem, if a minor one. We have for the first problem x <- 10^(ex <- c(1,2,5*(1:5),50,100,200,300,Inf)) ex <- -c(rev(1/x), ex) qcauchy(ex, log=TRUE) The first entry of the result should be Inf and the last -Inf. From the output you have shown us I would guess the last is NaN. If this is what is going on, it is a problem but a somewhat esoteric one that probably reflects a lack of IEC60559 (aka IEEE754) conformance. It needs more hands-on debugging than we can provide on a help list.
Thanks for the analysis. I'll move this over to r-devel. Jeff