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(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; 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>
wrote:
> 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.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
>> '
>> 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:
>>>
>>>
>>> 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://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://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@r-project.org <mailto:Bioc-devel@r-project.org>
>>> <Bioc-devel@r-project.org> mailing list
>>>
>>> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D&reserved=0
>>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D&reserved=0>
>>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C0e7c021440214cf1ba5708dc2362f85a%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638424155200977608%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=0x4xNPvAHnkGyUcEz4PVIOM8eCVTEWNpNUOkskspUEQ%3D&reserved=0>
>>> <
>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$>
>>> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
>>> <Bioc-devel@r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Bioconductor Core teamhpages.on.git...@gmail.com
>>>
>>>
>>>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
