[Bioc-devel] Incorrect warning about failing package built

Martin Grigorov m@rt|n@gr|gorov @end|ng |rom gm@||@com
Sun Feb 4 21:27:18 CET 2024 

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.griss using 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.Wokaty using sph.cuny.edu
> <mailto:Jennifer.Wokaty using sph.cuny.edu> <Jennifer.Wokaty using 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-bounces using r-project.org
>     <mailto:bioc-devel-bounces using r-project.org>
> <bioc-devel-bounces using r-project.org>> on behalf of Johannes
>     Griss <johannes.griss using meduniwien.ac.at
>     <mailto:johannes.griss using meduniwien.ac.at>
> <johannes.griss using meduniwien.ac.at>>
>     Sent: Thursday, February 1, 2024 3:18 PM
>     To: bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>
> <bioc-devel using r-project.org>
>     <bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>
> <bioc-devel using 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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> <
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> <
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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 using r-project.org <mailto:Bioc-devel using r-project.org>
> <Bioc-devel using r-project.org> mailing list
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