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
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>
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(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
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>>>> <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]]
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