[Bioc-devel] Incorrect warning about failing package built
Johannes Griss
joh@nne@@gr|@@ @end|ng |rom medun|w|en@@c@@t
Wed Feb 14 15:16:30 CET 2024
Hi Martin,
Thanks a lot for the help!
Kind regards,
Johannes
On 14.02.24 15:06, Martin Grigorov wrote:
> 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 <http://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.grigorov using gmail.com <mailto:martin.grigorov using 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
> <http://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
> <http://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.grigorov using gmail.com <mailto:martin.grigorov using gmail.com>> wrote:
>
> Hi,
>
> Here is the issue -
> https://github.com/TomKellyGenetics/leiden/issues/26
> <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 <mailto: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 <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
> <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 <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
> <http://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
> <http://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
> <mailto: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>
>>>> <mailto:Jennifer.Wokaty using sph.cuny.edu>
>>>> <mailto: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>
>>>> <mailto:bioc-devel-bounces using r-project.org>
>>>> <mailto: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>
>>>> <mailto:johannes.griss using meduniwien.ac.at>
>>>> <mailto: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>
>>>> <mailto:bioc-devel using r-project.org>
>>>> <mailto:bioc-devel using r-project.org>
>>>> <bioc-devel using r-project.org
>>>> <mailto:bioc-devel using r-project.org>
>>>> <mailto:bioc-devel using r-project.org>
>>>> <mailto: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 <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://urldefense.com/v3/__https://bioconductor.org/checkResults/release/bioc-LATEST/ReactomeGSA/__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0e-zXx6o$>>
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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>
>>>> <mailto:Bioc-devel using r-project.org>
>>>> <mailto:Bioc-devel using 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://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$> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!M-1zUaRSf4H_CKYUyhpGNOS9X3o9oI8ig_h2rck5yvFPc1mC4nbUNsLfyxRJNMbhmsAGjnS4E9GoK_LE2uqmKM0fkPMpu89nUSA0ArxoE98$>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org
>>>> <mailto:Bioc-devel using r-project.org>
>>>> <mailto:Bioc-devel using r-project.org>
>>>> <mailto:Bioc-devel using 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>
>>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org
>>> <mailto:Bioc-devel using r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>
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