Hi,
The issue has been resolved by not using the system's Python installation.
I.e. on kunpeng2 RETICULATE_PYTHON env var is no longer exported! The
reticulate package installs its own Python:
> reticulate::py_config()
python: /home/biocbuild/.virtualenvs/r-reticulate/bin/python
libpython: /usr/lib64/libpython3.9.so <http://libpython3.9.so>
pythonhome:
/home/biocbuild/.virtualenvs/r-reticulate:/home/biocbuild/.virtualenvs/r-reticulate
version: 3.9.9 (main, Oct 18 2023, 18:17:13) [GCC 10.3.1]
numpy:
/home/biocbuild/.virtualenvs/r-reticulate/lib/python3.9/site-packages/numpy
numpy_version: 1.26.3
ReactomeGSA.data is installed on kunpeng2!
Regards,
Martin
On Mon, Feb 5, 2024 at 12:08 PM Martin Grigorov
<martin.grigo...@gmail.com <mailto:martin.grigo...@gmail.com>> wrote:
Hi again,
I tried to find the problem by (un)installing any (pip) global
installations of pandas, leidenalg, umap-learn, igraph and
python-igraph, and then installing them with biocbuild's pip, i.e.
non-root user, via reticulate but the error persists!
Then I tried:
reticulate::py_module_available("numpy")
*** caught segfault ***
address 0x90, cause 'memory not mapped'
Traceback:
1: py_initialize(config$python, config$libpython,
config$pythonhome, config$virtualenv_activate, config$version >=
"3.0", interactive(), numpy_load_error)
2: (function() { Sys.setenv(PYTHONPATH = newpythonpath)
on.exit(Sys.setenv(PYTHONPATH = oldpythonpath), add = TRUE)
py_initialize(config$python, config$libpython, config$pythonhome,
config$virtualenv_activate, config$version >= "3.0",
interactive(), numpy_load_error)})()
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch({ oldpythonpath <- Sys.getenv("PYTHONPATH")
newpythonpath <- Sys.getenv("RETICULATE_PYTHONPATH", unset =
paste(config$pythonpath, system.file("python", package =
"reticulate"), sep = .Platform$path.sep)) local({
Sys.setenv(PYTHONPATH = newpythonpath)
on.exit(Sys.setenv(PYTHONPATH = oldpythonpath), add = TRUE)
py_initialize(config$python, config$libpython, config$pythonhome,
config$virtualenv_activate, config$version >= "3.0",
interactive(), numpy_load_error) })}, error =
function(e) { Sys.setenv(PATH = oldpath) if (is.na
<http://is.na>(curr_session_env)) {
Sys.unsetenv("R_SESSION_INITIALIZED") } else {
Sys.setenv(R_SESSION_INITIALIZED = curr_session_env) } stop(e)})
7: initialize_python()
8: ensure_python_initialized(required_module = module)
9: import(module)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch({ import(module) TRUE}, error =
clear_error_handler(FALSE))
14: reticulate::py_module_available("numpy")
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
That is, reticulate::py_module_available("XYZ") always fails with a
segfault.
> sessionInfo()
R Under development (unstable) (2024-01-16 r85812)
Platform: aarch64-unknown-linux-gnu
Running under: openEuler 22.03 (LTS-SP1)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.18.so
<http://libopenblas-r0.3.18.so>; LAPACK version 3.9.0
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_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reticulate_1.35.0
loaded via a namespace (and not attached):
[1] compiler_4.4.0 Matrix_1.6-5 cli_3.6.2 tools_4.4.0
Rcpp_1.0.12
[6] grid_4.4.0 jsonlite_1.8.8 rlang_1.1.3 png_0.1-8
lattice_0.22-5
On Mon, Feb 5, 2024 at 9:39 AM Martin Grigorov
<martin.grigo...@gmail.com <mailto:martin.grigo...@gmail.com>> wrote:
Hi,
Here is the issue -
https://github.com/TomKellyGenetics/leiden/issues/26
<https://github.com/TomKellyGenetics/leiden/issues/26>
I realized that we have discussed it a few months back!
Martin
On Sun, Feb 4, 2024 at 10:27 PM Martin Grigorov
<martin.grigo...@gmail.com <mailto:martin.grigo...@gmail.com>>
wrote:
Hi ,
ReactomeGSA.data package fails to install because it depends
on leiden and Seurat
> BiocManager::install("ReactomeGSA.data", force = TRUE)
Bioconductor version 3.19 (BiocManager 1.30.22), R Under
development (unstable)
(2024-01-16 r85812)
Installing package(s) 'ReactomeGSA.data'
also installing the dependencies ‘leiden’, ‘Seurat’
trying URL
'https://cloud.r-project.org/src/contrib/leiden_0.4.3.1.tar.gz
<https://cloud.r-project.org/src/contrib/leiden_0.4.3.1.tar.gz>'
Content type 'application/x-gzip' length 2864241 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
trying URL
'https://cloud.r-project.org/src/contrib/Seurat_5.0.1.tar.gz
<https://cloud.r-project.org/src/contrib/Seurat_5.0.1.tar.gz>'
Content type 'application/x-gzip' length 2225638 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL
'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/ReactomeGSA.data_1.17.1.tar.gz
<https://bioconductor.org/packages/3.19/data/experiment/src/contrib/ReactomeGSA.data_1.17.1.tar.gz>'
Content type 'application/x-gzip' length 24200519 bytes
(23.1 MB)
==================================================
downloaded 23.1 MB
* installing *source* package ‘leiden’ ...
** package ‘leiden’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary
location
*** caught segfault ***
address 0x90, cause 'memory not mapped'
Traceback:
1: py_initialize(config$python, config$libpython,
config$pythonhome, config$virtualenv_activate,
config$version >= "3.0", interactive(), numpy_load_error)
2: (function() { Sys.setenv(PYTHONPATH = newpythonpath)
on.exit(Sys.setenv(PYTHONPATH = oldpythonpath), add =
TRUE) py_initialize(config$python, config$libpython,
config$pythonhome, config$virtualenv_activate,
config$version >= "3.0", interactive(),
numpy_load_error)})()
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch({ oldpythonpath <- Sys.getenv("PYTHONPATH")
newpythonpath <- Sys.getenv("RETICULATE_PYTHONPATH",
unset = paste(config$pythonpath,
system.file("python", package = "reticulate"), sep =
.Platform$path.sep)) local({ Sys.setenv(PYTHONPATH
= newpythonpath) on.exit(Sys.setenv(PYTHONPATH =
oldpythonpath), add = TRUE)
py_initialize(config$python, config$libpython,
config$pythonhome, config$virtualenv_activate,
config$version >= "3.0", interactive(),
numpy_load_error) })}, error = function(e) {
Sys.setenv(PATH = oldpath) if (is.na
<http://is.na>(curr_session_env)) {
Sys.unsetenv("R_SESSION_INITIALIZED") } else {
Sys.setenv(R_SESSION_INITIALIZED = curr_session_env) }
stop(e)})
7: initialize_python()
8: ensure_python_initialized(required_module = module)
9: import(module)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch({ import(module) TRUE}, error =
clear_error_handler(FALSE))
14: reticulate::py_module_available("pandas")
15: fun(libname, pkgname)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(fun(libname, pkgname), error = identity)
20: runHook(".onAttach", ns, dirname(nspath), nsname)
21: attachNamespace(ns, pos = pos, deps, exclude, include.only)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch({ attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc) env <-
attachNamespace(ns, pos = pos, deps, exclude,
include.only)}, error = function(e) { P <- if
(!is.null(cc <- conditionCall(e))) paste(" in",
deparse(cc)[1L]) else "" msg <- gettextf("package or
namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e)) if
(logical.return && !quietly) message(paste("Error:",
msg), domain = NA) else stop(msg, call. = FALSE, domain =
NA)})
26: library(pkg_name, lib.loc = lib, character.only = TRUE,
logical.return = TRUE)
27: withCallingHandlers(expr, packageStartupMessage =
function(c) tryInvokeRestart("muffleMessage"))
28: suppressPackageStartupMessages(library(pkg_name, lib.loc
= lib, character.only = TRUE, logical.return = TRUE))
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(expr, error = function(e) { call <-
conditionCall(e) if (!is.null(call)) { if
(identical(call[[1L]], quote(doTryCatch))) call
<- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ") LONG
<- 75L sm <- strsplit(conditionMessage(e),
"\n")[[1L]] w <- 14L + nchar(dcall, type = "w") +
nchar(sm[1L], type = "w") if (is.na
<http://is.na>(w)) w <- 14L + nchar(dcall, type
= "b") + nchar(sm[1L], type = "b") if
(w > LONG) prefix <- paste0(prefix, "\n ") }
else prefix <- "Error : " msg <- paste0(prefix,
conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L])) if (!silent &&
isTRUE(getOption("show.error.messages"))) { cat(msg,
file = outFile) .Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error",
condition = e))})
33: try(suppressPackageStartupMessages(library(pkg_name,
lib.loc = lib, character.only = TRUE, logical.return =
TRUE)))
34: tools:::.test_load_package("leiden",
"/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/00LOCK-leiden/00new")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing
‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/leiden’
ERROR: dependency ‘leiden’ is not available for package ‘Seurat’
* removing
‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/Seurat’
ERROR: dependency ‘Seurat’ is not available for package
‘ReactomeGSA.data’
* removing
‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library/ReactomeGSA.data’
The downloaded source packages are in
‘/home/biocbuild/tmp/RtmpjFiqDm/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘leiden’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘Seurat’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘ReactomeGSA.data’ had non-zero
exit status
Any hints on what is the problem ?
Martin
On Fri, Feb 2, 2024 at 9:52 AM Griss Johannes
<johannes.gr...@meduniwien.ac.at
<mailto:johannes.gr...@meduniwien.ac.at>> wrote:
Dear Hervé,
Thanks a lot for the explanation and clarification!
Issue should be fixed by now.
Kind regards,
Johannes
Am 2024-02-02 01:37, schrieb Hervé Pagès:
Just to clarify: we build the vignettes on all
platforms, via 'R CMD build'. However when a package
contains more than one vignette like here, keep in
mind that 'R CMD build' evaluates them all in the same
R session. This "feature" can help a vignette succeed
even if it's broken. For example if ReactomeGSA got
loaded by a previous vignette then evaluation of
reanalysing-public-data.Rmd would still succeed even
though it doesn't do 'library(ReactomeGSA)'.
To complicate things even more, it could be that the
order in which vignettes are evaluated is
platform-dependent. This could explain why a vignette
succeeds on one platform and not the other.
Best,
H.
On 2/1/24 13:30, Johannes Griss wrote:
Hi,
Thanks a lot for the quick reply!
Vignette is already fixed and committed.
Kind regards,
Johannes
On 01.02.24 22:24, Martin Grigorov wrote:
Hi,
On Thu, 1 Feb 2024 at 23:05, Jennifer Wokaty
<jennifer.wok...@sph.cuny.edu
<mailto:jennifer.wok...@sph.cuny.edu>
<mailto:jennifer.wok...@sph.cuny.edu>
<mailto:jennifer.wok...@sph.cuny.edu>> wrote:
Hi Johannes,
Looking at R CMD Check on devel, it looks like
you're missing a
`library(ReactomeGSA)` in
reanalysing-public-data.Rmd, which is why
it doesn't find the function
`get_public_species()`. We only build
the vignettes on the Linux builders, which this
error is only caught
there.
Regarding the error kunpeng2, we could ask its
maintainer to install
ReactomeGSA.data, which appears to be missing.
If this happens
again, you can reach out to Martin on the Bioc
Community Slack
channel #arm-linux. He's very active and
responsive.
I will take a look early next week!
Martin
Lastly, regarding the notification that happened
on the 2024/01/08,
it's possible that it failed due to an issue
with another package at
that time which has since been resolved.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel
<bioc-devel-boun...@r-project.org
<mailto:bioc-devel-boun...@r-project.org>
<mailto:bioc-devel-boun...@r-project.org>
<mailto:bioc-devel-boun...@r-project.org>> on behalf
of Johannes
Griss <johannes.gr...@meduniwien.ac.at
<mailto:johannes.gr...@meduniwien.ac.at>
<mailto:johannes.gr...@meduniwien.ac.at>
<mailto:johannes.gr...@meduniwien.ac.at>>
Sent: Thursday, February 1, 2024 3:18 PM
To: bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>
<bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>
<mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Incorrect warning about
failing package built
* This email originates from a sender outside of
CUNY. Verify the
sender before replying or clicking on links and
attachments. *
Hello,
I just received a second warning the our package
ReactomeGSA is failing
in both release and devel on all platforms.
Quickly checking the respective reports shows
that this is not the case:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200958363%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tbYEx3lk0V%2BBLNUdbLHtclDpeGm9sq5W7Tv9lK%2BnNx8%3D&reserved=0
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On release we have no errors or warnings at all,
on devel, everything is
fine in two instances while the others seem to
have issues that we will
look into.
Is there anything I can do to fix that?
Kind regards,
Johannes
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