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'
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'
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
'
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(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(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> 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> <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>
> <bioc-devel-boun...@r-project.org>> on behalf of Johannes
> Griss <johannes.gr...@meduniwien.ac.at
> <mailto:johannes.gr...@meduniwien.ac.at>
> <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>
> <bioc-devel@r-project.org>
> <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>
> <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:
>
>
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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
>
> _______________________________________________
> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> <Bioc-devel@r-project.org> mailing list
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