Hi Martin,
On 17 February 2021 at 10:43, Martin Maechler wrote:
| Dear Dirk,
| I'm in vacations right now ...
Ah, nice.
| 1) I think I might simply disable the check *on* that platform .. or
| platforms with similar characteristics.
Sounds good to me.
| Can you send me the outputs of so I can take some of the entries to
| determine I'm on the platform?
|
| sessionInfo()
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: s390x-ibm-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid
Matrix products: default
BLAS: /usr/lib/s390x-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.3
>
| str(.Machine, digits=10)
> str(.Machine, digits=10)
List of 28
$ double.eps : num 2.220446049e-16
$ double.neg.eps : num 1.110223025e-16
$ double.xmin : num 2.225073859e-308
$ double.xmax : num 1.797693135e+308
$ double.base : int 2
$ double.digits : int 53
$ double.rounding : int 5
$ double.guard : int 0
$ double.ulp.digits : int -52
$ double.neg.ulp.digits : int -53
$ double.exponent : int 11
$ double.min.exp : int -1022
$ double.max.exp : int 1024
$ integer.max : int 2147483647
$ sizeof.long : int 8
$ sizeof.longlong : int 8
$ sizeof.longdouble : int 16
$ sizeof.pointer : int 8
$ longdouble.eps : num 1.925929944e-34
$ longdouble.neg.eps : num 9.629649722e-35
$ longdouble.digits : int 113
$ longdouble.rounding : int 5
$ longdouble.guard : int 0
$ longdouble.ulp.digits : int -112
$ longdouble.neg.ulp.digits: int -113
$ longdouble.exponent : int 15
$ longdouble.min.exp : int -16382
$ longdouble.max.exp : int 16384
>
| capabilities()
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE TRUE TRUE
NLS profmem cairo ICU long.double libcurl
TRUE TRUE TRUE TRUE TRUE TRUE
>
| .Platform
> str(.Platform)
List of 8
$ OS.type : chr "unix"
$ file.sep : chr "/"
$ dynlib.ext: chr ".so"
$ GUI : chr "X11"
$ endian : chr "big"
$ pkgType : chr "source"
$ path.sep : chr ":"
$ r_arch : chr ""
>
| 2) Can you send me the result of rankMatrix(Z, method="qr")
| i.e. `rnkZ.` from the above example ?
> library(Matrix)
> Z. <- readRDS(system.file("external", "Z_NA_rnk.rds", package="Matrix"))
> rnkZ. <- rankMatrix(Z., method = "qr")
> rnkZ.
[1] 724
attr(,"method")
[1] "qr.R"
attr(,"useGrad")
[1] FALSE
attr(,"tol")
[1] 3.126388e-13
>
Graham (in subsequent message) makes a good point about big endian. Maybe we
need a slightly wider net.
It could, as always, of course be something else but related. I could replace
the default BLAS with OpenBLAS etc but ex ante the default BLAS should work :-/
But as you hinted, if we skip that one test on this one architecture it
passes. I used a very minimal diff (below) and quickly rebuilt (by skipping
vignettes as I currently do not have texlive installed on the s390x (but
could add it)).
(sid_s390x-dchroot)edd@zelenka:/tmp/downloaded_packages$ diff -u
Matrix{,.orig}/tests/factorizing.R
--- Matrix/tests/factorizing.R 2021-02-17 13:01:06.511757335 +0000
+++ Matrix.orig/tests/factorizing.R 2021-01-04 20:32:35.000000000 +0000
@@ -472,7 +472,6 @@
})
options(oo)
-if (Sys.info()[["machine"]] != "s390x") {
## problematic rank deficient rankMatrix() case -- only seen in large cases ??
Z. <- readRDS(system.file("external", "Z_NA_rnk.rds", package="Matrix"))
tools::assertWarning(rnkZ. <- rankMatrix(Z., method = "qr")) # gave errors
@@ -482,7 +481,6 @@
oo <- options(warn=2)# no warnings allowed from here
di <- diag(qrZ.@R)
stopifnot(is.na(rnkZ.), is(qrZ, "sparseQR"), is.na(rnk2), anyNA(di))
-}
## The above bug fix was partly wrongly extended to dense matrices for "qr.R":
x <- cbind(1, rep(0:9, 18))
(sid_s390x-dchroot)edd@zelenka:/tmp/downloaded_packages$
(Obviously the if above could be indentented and all that.)
Graham: What does that bigendian box say for Sys.info()[["machine"]] ?
Should we test for endianness instead? And then maybe try to roll up to the
cause of the difference?
Dirk
| Best, Martin
|
| On Mon, Feb 15, 2021 at 5:12 PM Dirk Eddelbuettel <e...@debian.org> wrote:
| >
| >
| > Martin,
| >
| > I have this long-running bug report against Matrix, triggered by glmmTMB on
| > s390x. Graham has been chasing this patiently and we are now at the level
of
| > checking on a shell account on the appropriate hardware.
| >
| > We validated that everything does in fact "still break" with CRAN-current
| > packages of everything (and R 4.0.3, I guess by tomorrow we'd have 4.0.4).
| >
| > glmmTMB does indeed fail in an example -- but so does Matrix 1.3-2 when I
run
| >
| > _R_CHECK_FORCE_SUGGESTS_=false R CMD check \
| > --no-manual --no-vignettes Matrix_1.3-2.tar.gz
| >
| > and I see
| >
| > [...]
| > Running 'factorizing.R'
| > ERROR
| > Running the tests in 'tests/factorizing.R' failed.
| > Last 13 lines of output:
| > + inherits(qrZ, "sparseQR")
| > + inherits(Rz, "sparseMatrix")
| > + isTriangular(Rz)
| > + isDiagonal(Rz) # even though formally a "dtCMatrix"
| > + qr2rankMatrix(qrZ, do.warn=FALSE) == 6
| > + })
| > > options(oo)
| > >
| > > ## problematic rank deficient rankMatrix() case -- only seen in large
cases ??
| > > Z. <- readRDS(system.file("external", "Z_NA_rnk.rds", package="Matrix"))
| > > tools::assertWarning(rnkZ. <- rankMatrix(Z., method = "qr")) # gave
errors
| > Error in assertCondition(expr, classes, .exprString = d.expr) :
| > Failed to get warning in evaluating rnkZ. <- rankMatrix(Z., method ...
| > Calls: <Anonymous> -> assertCondition
| > Execution halted
| > * checking for unstated dependencies in vignettes ... OK
| >
| > Can you advise if I should dive into a particular routine or comparison to
| > see what is up here?
| >
| > Best, Dirk
| >
| > --
| > https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| >
|
|
| --
| Martin Maechler,
| Seminar fuer Statistik, ETH Zurich
--
https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
