Binary files /tmp/tmpw9ieioia/PH9IBDLj66/r-bioc-annotationhub-3.2.2+dfsg/build/vignette.rds and /tmp/tmpw9ieioia/hurk_KmXLo/r-bioc-annotationhub-3.4.0+dfsg/build/vignette.rds differ diff -Nru r-bioc-annotationhub-3.2.2+dfsg/debian/changelog r-bioc-annotationhub-3.4.0+dfsg/debian/changelog --- r-bioc-annotationhub-3.2.2+dfsg/debian/changelog 2022-03-08 11:33:48.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/debian/changelog 2022-05-16 04:52:39.000000000 +0000 @@ -1,3 +1,11 @@ +r-bioc-annotationhub (3.4.0+dfsg-1) unstable; urgency=medium + + * Team upload. + * New upstream version 3.4.0+dfsg + * Bump Standards-Version to 4.6.1 (no changes needed) + + -- Nilesh Patra Mon, 16 May 2022 10:22:39 +0530 + r-bioc-annotationhub (3.2.2+dfsg-1) unstable; urgency=medium * New upstream version diff -Nru r-bioc-annotationhub-3.2.2+dfsg/debian/control r-bioc-annotationhub-3.4.0+dfsg/debian/control --- r-bioc-annotationhub-3.2.2+dfsg/debian/control 2022-03-08 11:33:48.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/debian/control 2022-05-16 04:52:17.000000000 +0000 @@ -20,7 +20,7 @@ r-cran-httr, r-cran-yaml, r-cran-dplyr -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-annotationhub Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-annotationhub.git Homepage: https://bioconductor.org/packages/AnnotationHub/ diff -Nru r-bioc-annotationhub-3.2.2+dfsg/DESCRIPTION r-bioc-annotationhub-3.4.0+dfsg/DESCRIPTION --- r-bioc-annotationhub-3.2.2+dfsg/DESCRIPTION 2022-03-01 08:46:36.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/DESCRIPTION 2022-04-26 20:00:06.000000000 +0000 @@ -1,7 +1,7 @@ Package: AnnotationHub Type: Package Title: Client to access AnnotationHub resources -Version: 3.2.2 +Version: 3.4.0 Authors@R: c(person("Bioconductor Package", "Maintainer", email="maintainer@bioconductor.org", role="cre"), @@ -42,11 +42,11 @@ BugReports: https://github.com/Bioconductor/AnnotationHub/issues NeedsCompilation: yes git_url: https://git.bioconductor.org/packages/AnnotationHub -git_branch: RELEASE_3_14 -git_last_commit: 8e761e1 -git_last_commit_date: 2022-02-28 -Date/Publication: 2022-03-01 -Packaged: 2022-03-01 08:46:36 UTC; biocbuild +git_branch: RELEASE_3_15 +git_last_commit: e74e54c +git_last_commit_date: 2022-04-26 +Date/Publication: 2022-04-26 +Packaged: 2022-04-26 20:00:06 UTC; biocbuild Author: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Marc Carlson [ctb], diff -Nru r-bioc-annotationhub-3.2.2+dfsg/inst/doc/AnnotationHub.Rmd r-bioc-annotationhub-3.4.0+dfsg/inst/doc/AnnotationHub.Rmd --- r-bioc-annotationhub-3.2.2+dfsg/inst/doc/AnnotationHub.Rmd 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/inst/doc/AnnotationHub.Rmd 2022-04-26 18:04:50.000000000 +0000 @@ -230,11 +230,18 @@ # Creating an AnnotationHub Package or Converting to an AnnotationHub Package -Please see HubPub Vignette "CreateAHubPackage". +Please see `r Biocpkg("HubPub")` Vignette "CreateAHubPackage". ``` vignette("CreateAHubPackage", package="HubPub") ``` +# Troubleshooting + +Please see AnnotationHub vignette "TroubleshootingTheCache". +``` +vignette("TroubleshootingTheCache", package=AnnotationHub) +``` + # Session info diff -Nru r-bioc-annotationhub-3.2.2+dfsg/inst/doc/TroubleshootingTheCache.Rmd r-bioc-annotationhub-3.4.0+dfsg/inst/doc/TroubleshootingTheCache.Rmd --- r-bioc-annotationhub-3.2.2+dfsg/inst/doc/TroubleshootingTheCache.Rmd 2022-01-22 11:57:04.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/inst/doc/TroubleshootingTheCache.Rmd 2022-04-26 18:04:50.000000000 +0000 @@ -357,6 +357,26 @@ available. If this was part of a subset to download, remove the resource id from the subset. +## Offline localHub usage + +There is a flag in the constructor `localHub=TRUE` to use only show previously +downloaded resources. If you are using this in an offline setting, please also +see the [BiocManager vignette on offline +use](https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#offline-use). The +Hubs use BiocManager::version to filter resources appropriate for your current +version of R/Bioconductor; therefore the offline usage of BiocManager needs to +be established. +The error that occurs that likely needs offline set up will look similar to the +following: + +``` +ExperimentHub(localHub=TRUE) +Error: failed to connect to local data base +database: ‘/home/user/.cache/R/ExperimentHub/24dc84dbf615e_experimenthub.sqlite3’ +reason: invalid version specification ‘Bioconductor version cannot be validated; no internet connection?’` + +``` + # Group Hub/Cache Access @@ -379,6 +399,39 @@ permissions. +# Lock file Troubleshooting + +Two issues have been commonly reported regarding the lock file. + +## Permissions + +There could be permission ERROR regarding group and public access. See the +previous `Group Cache Access` section. + +## Cannot lock file / no lock available + +This is an issue with filelock on particular systems. Particular partitions and +non standard file systems may not support filelock. The solution is to use a +different section of the system to create the cache. The easiest way to define a +new cache location is by using environment variables. + +In R: + +`Sys.setenv(BFC_CACHE=)` + +Alternatively, you can set an environment variable globally to avoid having to +set uniquely in each R session. Please google for specific instructions for +setting environment variables globally for your particular OS system. + +Other common filelock implemented packages that have specific environment +variables to control location are: + + * BiocFileCache: BFC_CACHE + * ExperimentHub: EXPERIMENT_HUB_CACHE + * AnnotationHub: ANNOTATION_HUB_CACHE + * biomaRt: BIOMART_CACHE + + # Default Caching Location Update diff -Nru r-bioc-annotationhub-3.2.2+dfsg/inst/unitTests/test_hub_options.R r-bioc-annotationhub-3.4.0+dfsg/inst/unitTests/test_hub_options.R --- r-bioc-annotationhub-3.2.2+dfsg/inst/unitTests/test_hub_options.R 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/inst/unitTests/test_hub_options.R 2022-04-26 18:04:50.000000000 +0000 @@ -1,6 +1,6 @@ test_option_key <- function(){ - checkIdentical(.hub_option_key("TESTING"), "TESTING") + checkIdentical(.hub_option_key("ASK"), "ASK") checkException(.hub_option_key("NOTFOUND")) } @@ -16,13 +16,7 @@ checkException(setAnnotationHubOption("NOTFOUND")) orig_max <- getAnnotationHubOption("MAX_DOWNLOADS") - orig_test <- getAnnotationHubOption("TESTING") setAnnotationHubOption("MAX_DOWNLOADS",100) checkIdentical(getAnnotationHubOption("MAX_DOWNLOADS"), 100L) setAnnotationHubOption("MAX_DOWNLOADS",orig_max) - setAnnotationHubOption("TESTING", TRUE) - checkIdentical(getAnnotationHubOption("TESTING"), TRUE) - setAnnotationHubOption("TESTING", FALSE) - checkIdentical(getAnnotationHubOption("TESTING"), FALSE) - setAnnotationHubOption("TESTING", orig_test) } diff -Nru r-bioc-annotationhub-3.2.2+dfsg/man/AnnotationHub-class.Rd r-bioc-annotationhub-3.4.0+dfsg/man/AnnotationHub-class.Rd --- r-bioc-annotationhub-3.2.2+dfsg/man/AnnotationHub-class.Rd 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/man/AnnotationHub-class.Rd 2022-04-26 18:04:50.000000000 +0000 @@ -99,9 +99,11 @@ Use \code{AnnotationHub()} to retrieve information about all records in the hub. If working offline, add argument \code{localHub=TRUE} to work with a local, non-updated hub; It will only have resources - available that have previously been downloaded. To force redownload of - the hub, \code{refreshHub(hubClass="AnnotationHub")} can be utilized. - + available that have previously been downloaded. If offline, Please + also see BiocManager vignette section on offline use to ensure proper + funcionality. To force redownload of the hub, + \code{refreshHub(hubClass="AnnotationHub")} can be utilized. + Discover records in a hub using \code{mcols()}, \code{query()}, \code{subset()}, \code{[}, and \code{display()}. @@ -121,6 +123,10 @@ The location of the local cache can be found (and updated) with \code{getAnnotationHubCache} and \code{setAnnotationHubCache}; \code{removeCache} removes all cache resources. + + For common hub troubleshooting, please see the AnnotationHub vignette + entitled `vignette("TroubleshootingTheCache", package=AnnotationHub)`. + } \section{Constructors}{ diff -Nru r-bioc-annotationhub-3.2.2+dfsg/man/getAnnotationHubOption.Rd r-bioc-annotationhub-3.4.0+dfsg/man/getAnnotationHubOption.Rd --- r-bioc-annotationhub-3.2.2+dfsg/man/getAnnotationHubOption.Rd 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/man/getAnnotationHubOption.Rd 2022-04-26 18:04:50.000000000 +0000 @@ -50,14 +50,6 @@ specified by \code{http://username:password@proxy.dom.com:8080}; \code{username:password} and port (e.g. \code{:8080}) are optional.} - \item{\dQuote{TESTING}:}{logical(1). TRUE/FALSE should the AnnotationHub - testing environment be used. AnnotationHub does automatic - filtering particularly with regards to OrgDbs. The - \code{TESTING=TRUE} setting will allow for all OrgDbs for a given - devel version to also be displayed. (This option should really - only be set by a OrgDb contributing maintainer for testing and - debugging). Default: FALSE.} - \item{\dQuote{LOCAL}:}{logical(1). TRUE/FALSE should the AnnotationHub create a hub consisting only of previously downloaded resourcesd. Default: FALSE.} diff -Nru r-bioc-annotationhub-3.2.2+dfsg/NEWS r-bioc-annotationhub-3.4.0+dfsg/NEWS --- r-bioc-annotationhub-3.2.2+dfsg/NEWS 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/NEWS 2022-04-26 18:04:50.000000000 +0000 @@ -1,3 +1,24 @@ +CHANGES IN VERSION 3.3.0 +------------------------- + +NEW FEATURES + + o (3.3.6) Serialized S4 hub resources (AnnotationHub and ExperimentHub) + are now passed thru updateObject() at load-time + +USER-VISIBLE MODIFICATIONS + + o (3.3.8) Add instructions for creating a hub shared across multiple users + o (3.3.2) Remove TESTING option as only needed to expose devel orgdb + o (3.3.2) Change filter for orgdbs. orgdbs at release time will be stamped + with devel (to be release) and then manually have biocversion added for the + upcoming new devel. Filtering then based on biocversion number. This will + expose devel orgdbs as soon as generated + +BUG CORRECTION + + o (3.1.9) Fix broken test. Identical not appropriate. all present appropriate + CHANGES IN VERSION 3.1.0 ------------------------- diff -Nru r-bioc-annotationhub-3.2.2+dfsg/R/AnnotationHub-class.R r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHub-class.R --- r-bioc-annotationhub-3.2.2+dfsg/R/AnnotationHub-class.R 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHub-class.R 2022-04-26 18:04:50.000000000 +0000 @@ -50,6 +50,10 @@ message("Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead") localHub <- !connect } + if(localHub){ + message("Using 'localHub=TRUE'\n", + " If offline, please also see BiocManager vignette section on offline use") + } .Hub("AnnotationHub", hub, cache, proxy, localHub, ask, ...) } diff -Nru r-bioc-annotationhub-3.2.2+dfsg/R/AnnotationHubOption.R r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHubOption.R --- r-bioc-annotationhub-3.2.2+dfsg/R/AnnotationHubOption.R 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHubOption.R 2022-04-26 18:04:50.000000000 +0000 @@ -8,7 +8,7 @@ .AH_hub_options <- new.env(parent=emptyenv()) .hub_option_key <- function(key0=c("URL", "CACHE", "PROXY", "MAX_DOWNLOADS", - "LOCAL", "TESTING", "ASK")) + "LOCAL", "ASK")) match.arg(key0) getAnnotationHubOption <- function(arg) { @@ -38,9 +38,6 @@ character(1), or NULL" stop(paste(strwrap(txt, exdent=2), collapse="\n")) } - }, TESTING={ - stopifnot(isTRUE(value) || isFALSE(value)) - value }, LOCAL={ stopifnot(isTRUE(value) || isFALSE(value)) value diff -Nru r-bioc-annotationhub-3.2.2+dfsg/R/AnnotationHubResource-class.R r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHubResource-class.R --- r-bioc-annotationhub-3.2.2+dfsg/R/AnnotationHubResource-class.R 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/R/AnnotationHubResource-class.R 2022-04-26 18:04:50.000000000 +0000 @@ -50,6 +50,34 @@ stop(paste(strwrap(msg), collapse="\n")) }) +.updateObject <- function(x) +{ + if (isS4(x)) { + ## Make sure that the package where the class of 'x' is defined is + ## loaded before calling 'updateObject()' on 'x'. We should normally + ## be able to rely on 'attr(class(x), "package")' to get the name of + ## that package. However, it seems that for some hub resources + ## 'attr(class(x), "package")' is set to ".GlobalEnv" rather than to + ## the name of that package. This is the case for example for + ## CellMapperList instances EH170 to EH175 in ExperimentHub. Not + ## sure how that's allowed but let's just deal with it. + classdef_pkg <- attr(class(x), "package") + if (!(is.null(classdef_pkg) || identical(classdef_pkg, ".GlobalEnv"))) + .require(classdef_pkg) + } + ## Make sure to use 'check=FALSE' to skip validation of the returned + ## object. The reason we want to skip validation is because 'validObject()' + ## is broken on some S3 objects e.g. on igraph objects: + ## ah <- AnnotationHub() + ## x <- ah[["AH60903"]] + ## class(x) # igraph + ## validObject(x) + ## Error in .classEnv(classDef) : + ## trying to get slot "package" from an object of a basic class ("NULL") + ## with no slots + updateObject(x, check=FALSE) +} + ## ## implementations ## @@ -83,7 +111,11 @@ ## Michael's AHCytoData is the only package (I think) that uses RDS. ## Added Rds to be compatible with Rda naming scheme. setClass("RdsResource", contains="AnnotationHubResource") -setMethod(".get1", "RdsResource", function(x, ...) readRDS(cache(getHub(x)))) +setMethod(".get1", "RdsResource", + function(x, ...) +{ + .updateObject(readRDS(cache(getHub(x)))) +}) setClass("RDSResource", contains="RdsResource") setMethod(".get1", "RDSResource", function(x, ...) callNextMethod(x, ...)) @@ -94,7 +126,7 @@ setMethod(".get1", "RdaResource", function(x, ...) { - get(load(cache(getHub(x)))) + .updateObject(get(load(cache(getHub(x))))) }) setClass("data.frameResource", contains="RdaResource") diff -Nru r-bioc-annotationhub-3.2.2+dfsg/R/sql-utils.R r-bioc-annotationhub-3.4.0+dfsg/R/sql-utils.R --- r-bioc-annotationhub-3.2.2+dfsg/R/sql-utils.R 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/R/sql-utils.R 2022-04-26 18:04:50.000000000 +0000 @@ -75,37 +75,16 @@ ## NOTE: Because OrgDbs are valid for a full devel cycle they are ## not filtered by snapshotDate(); the OrgDbs are valid for all - if(curl::has_internet() || !localHub){ - isDevel <- BiocManager:::isDevel() - orgdb_release_version <- - if (getAnnotationHubOption("TESTING") || !isDevel) { - BiocManager::version() - } else { - BiocManager:::.version_bioc("release") - } - - query2 <- sprintf( - 'SELECT resources.id - FROM resources, biocversions, rdatapaths - WHERE biocversions.biocversion == "%s" - AND rdatapaths.rdataclass == "OrgDb" - AND resources.rdatadateremoved IS NULL - AND biocversions.resource_id == resources.id - AND rdatapaths.resource_id == resources.id', - orgdb_release_version) - biocIds2 <- .db_query(conn, query2)[[1]] - }else{ - query2 <- sprintf( - 'SELECT resources.id + query2 <- sprintf( + 'SELECT resources.id FROM resources, biocversions, rdatapaths WHERE biocversions.biocversion == "%s" AND rdatapaths.rdataclass == "OrgDb" AND resources.rdatadateremoved IS NULL AND biocversions.resource_id == resources.id AND rdatapaths.resource_id == resources.id', - BiocManager::version()) - biocIds2 <- .db_query(conn, query2)[[1]] - } + BiocManager::version()) + biocIds2 <- .db_query(conn, query2)[[1]] ## make unique and sort diff -Nru r-bioc-annotationhub-3.2.2+dfsg/R/zzz.R r-bioc-annotationhub-3.4.0+dfsg/R/zzz.R --- r-bioc-annotationhub-3.2.2+dfsg/R/zzz.R 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/R/zzz.R 2022-04-26 18:04:50.000000000 +0000 @@ -26,12 +26,6 @@ if (nzchar(opt)) setAnnotationHubOption("PROXY", opt) } - if (is.null(getAnnotationHubOption("TESTING"))) { - opt <- getOption("ANNOTATION_HUB_TESTING", FALSE) - opt <- Sys.getenv("ANNOTATION_HUB_TESTING", opt) - opt <- as.logical(opt) - setAnnotationHubOption("TESTING", opt) - } if (is.null(getAnnotationHubOption("LOCAL"))) { opt <- getOption("ANNOTATION_HUB_LOCAL", FALSE) opt <- Sys.getenv("ANNOTATION_HUB_LOCAL", opt) diff -Nru r-bioc-annotationhub-3.2.2+dfsg/vignettes/AnnotationHub.Rmd r-bioc-annotationhub-3.4.0+dfsg/vignettes/AnnotationHub.Rmd --- r-bioc-annotationhub-3.2.2+dfsg/vignettes/AnnotationHub.Rmd 2021-10-26 19:00:46.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/vignettes/AnnotationHub.Rmd 2022-04-26 18:04:50.000000000 +0000 @@ -230,11 +230,18 @@ # Creating an AnnotationHub Package or Converting to an AnnotationHub Package -Please see HubPub Vignette "CreateAHubPackage". +Please see `r Biocpkg("HubPub")` Vignette "CreateAHubPackage". ``` vignette("CreateAHubPackage", package="HubPub") ``` +# Troubleshooting + +Please see AnnotationHub vignette "TroubleshootingTheCache". +``` +vignette("TroubleshootingTheCache", package=AnnotationHub) +``` + # Session info diff -Nru r-bioc-annotationhub-3.2.2+dfsg/vignettes/TroubleshootingTheCache.Rmd r-bioc-annotationhub-3.4.0+dfsg/vignettes/TroubleshootingTheCache.Rmd --- r-bioc-annotationhub-3.2.2+dfsg/vignettes/TroubleshootingTheCache.Rmd 2022-01-22 11:57:04.000000000 +0000 +++ r-bioc-annotationhub-3.4.0+dfsg/vignettes/TroubleshootingTheCache.Rmd 2022-04-26 18:04:50.000000000 +0000 @@ -357,6 +357,26 @@ available. If this was part of a subset to download, remove the resource id from the subset. +## Offline localHub usage + +There is a flag in the constructor `localHub=TRUE` to use only show previously +downloaded resources. If you are using this in an offline setting, please also +see the [BiocManager vignette on offline +use](https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#offline-use). The +Hubs use BiocManager::version to filter resources appropriate for your current +version of R/Bioconductor; therefore the offline usage of BiocManager needs to +be established. +The error that occurs that likely needs offline set up will look similar to the +following: + +``` +ExperimentHub(localHub=TRUE) +Error: failed to connect to local data base +database: ‘/home/user/.cache/R/ExperimentHub/24dc84dbf615e_experimenthub.sqlite3’ +reason: invalid version specification ‘Bioconductor version cannot be validated; no internet connection?’` + +``` + # Group Hub/Cache Access @@ -379,6 +399,39 @@ permissions. +# Lock file Troubleshooting + +Two issues have been commonly reported regarding the lock file. + +## Permissions + +There could be permission ERROR regarding group and public access. See the +previous `Group Cache Access` section. + +## Cannot lock file / no lock available + +This is an issue with filelock on particular systems. Particular partitions and +non standard file systems may not support filelock. The solution is to use a +different section of the system to create the cache. The easiest way to define a +new cache location is by using environment variables. + +In R: + +`Sys.setenv(BFC_CACHE=)` + +Alternatively, you can set an environment variable globally to avoid having to +set uniquely in each R session. Please google for specific instructions for +setting environment variables globally for your particular OS system. + +Other common filelock implemented packages that have specific environment +variables to control location are: + + * BiocFileCache: BFC_CACHE + * ExperimentHub: EXPERIMENT_HUB_CACHE + * AnnotationHub: ANNOTATION_HUB_CACHE + * biomaRt: BIOMART_CACHE + + # Default Caching Location Update