[Bioc-devel] Incorrect warning about failing package built

Martin Grigorov m@rt|n@gr|gorov @end|ng |rom gm@||@com
Mon Feb 5 08:39:48 CET 2024 

Hi,

Here is the issue - 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.grigorov using 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'
> 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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>> <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>
>> <
>> https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$
>> <https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$>
>> <https://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$>>
>>
>>
>> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0>
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FReactomeGSA%2F__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200973059%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=EZnvSQ0zSzlNuW5DocjOsROuDVk6e7GH0Hg%2ByRnhdwQ%3D&reserved=0>
>> <
>> https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$
>> <https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$>
>> <https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0rnxJ23U$>>
>>
>>
>>     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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