From a3b25f8e7e24e834a57c28a324f31ef0fcd58df3 Mon Sep 17 00:00:00 2001 From: danlu1 Date: Wed, 21 Aug 2024 01:06:32 +0000 Subject: [PATCH] patch release to pin rjson version and update of installation instruction --- DESCRIPTION | 4 +- Dockerfile | 2 +- Dockerfile.rstudio | 2 +- NEWS.md | 5 + README.Rmd | 4 +- README.md | 4 +- docs/404.html | 4 +- docs/ISSUE_TEMPLATE.html | 4 +- docs/LICENSE-text.html | 4 +- docs/articles/docker.html | 8 +- docs/articles/index.html | 4 +- docs/articles/installation.html | 14 +- docs/articles/manageSynapseCredentials.html | 6 +- docs/articles/synapser.html | 140 +++++++++--------- docs/articles/systemDependencies.html | 6 +- docs/articles/tables.html | 18 +-- docs/articles/troubleshooting.html | 6 +- docs/articles/upload.html | 6 +- docs/articles/views.html | 36 ++--- docs/authors.html | 18 ++- docs/index.html | 11 +- docs/news/index.html | 20 ++- docs/pkgdown.yml | 2 +- docs/reference/Activity-class.html | 4 +- docs/reference/Activity.html | 4 +- docs/reference/Column-class.html | 4 +- docs/reference/Column.html | 4 +- docs/reference/Dataset-class.html | 4 +- docs/reference/Dataset.html | 4 +- docs/reference/DockerRepository-class.html | 4 +- docs/reference/DockerRepository.html | 4 +- docs/reference/EntityViewSchema-class.html | 4 +- docs/reference/EntityViewSchema.html | 4 +- docs/reference/Evaluation-class.html | 4 +- docs/reference/Evaluation.html | 4 +- docs/reference/File-class.html | 4 +- docs/reference/File.html | 4 +- docs/reference/Folder-class.html | 4 +- docs/reference/Folder.html | 4 +- docs/reference/Link-class.html | 4 +- docs/reference/Link.html | 4 +- .../MaterializedViewSchema-class.html | 4 +- docs/reference/MaterializedViewSchema.html | 4 +- docs/reference/PartialRowset-class.html | 4 +- docs/reference/PartialRowset.html | 4 +- docs/reference/Project-class.html | 4 +- docs/reference/Project.html | 4 +- docs/reference/Row-class.html | 4 +- docs/reference/Row.html | 4 +- docs/reference/RowSet-class.html | 4 +- docs/reference/RowSet.html | 4 +- docs/reference/Schema-class.html | 4 +- docs/reference/Schema.html | 4 +- docs/reference/Submission-class.html | 4 +- docs/reference/Submission.html | 4 +- docs/reference/SubmissionStatus-class.html | 4 +- docs/reference/SubmissionStatus.html | 4 +- .../reference/SubmissionViewSchema-class.html | 4 +- docs/reference/SubmissionViewSchema.html | 4 +- docs/reference/Table.html | 4 +- docs/reference/Team-class.html | 4 +- docs/reference/Team.html | 4 +- docs/reference/TeamMember-class.html | 4 +- docs/reference/TeamMember.html | 4 +- docs/reference/UserGroupHeader-class.html | 4 +- docs/reference/UserGroupHeader.html | 4 +- docs/reference/UserProfile-class.html | 4 +- docs/reference/UserProfile.html | 4 +- docs/reference/Wiki-class.html | 4 +- docs/reference/Wiki.html | 4 +- docs/reference/as.list.html | 4 +- docs/reference/index.html | 4 +- docs/reference/nextElem.html | 4 +- docs/reference/synBuildTable.html | 4 +- docs/reference/synClearDownloadList.html | 4 +- docs/reference/synCreateColumn.html | 4 +- docs/reference/synCreateColumns.html | 4 +- .../synCreateExternalS3FileHandle.html | 4 +- .../reference/synCreateS3StorageLocation.html | 4 +- docs/reference/synCreateSnapshotVersion.html | 4 +- .../synCreateStorageLocationSetting.html | 4 +- docs/reference/synCreateTeam.html | 4 +- docs/reference/synDelete.html | 4 +- docs/reference/synDeleteProvenance.html | 4 +- docs/reference/synDeleteTeam.html | 4 +- docs/reference/synDownloadTableColumns.html | 4 +- docs/reference/synFindEntityId.html | 4 +- docs/reference/synGet.html | 4 +- docs/reference/synGetAnnotations.html | 4 +- docs/reference/synGetChildren.html | 4 +- docs/reference/synGetColumn.html | 4 +- docs/reference/synGetColumns.html | 4 +- docs/reference/synGetConfigFile.html | 4 +- docs/reference/synGetDownloadList.html | 4 +- .../reference/synGetDownloadListManifest.html | 4 +- docs/reference/synGetEvaluation.html | 4 +- .../synGetEvaluationByContentSource.html | 4 +- docs/reference/synGetEvaluationByName.html | 4 +- docs/reference/synGetMembershipStatus.html | 4 +- .../synGetMyStorageLocationSetting.html | 4 +- docs/reference/synGetPermissions.html | 4 +- docs/reference/synGetProjectSetting.html | 4 +- docs/reference/synGetProvenance.html | 4 +- docs/reference/synGetStsStorageToken.html | 4 +- docs/reference/synGetSubmission.html | 4 +- docs/reference/synGetSubmissionBundles.html | 4 +- docs/reference/synGetSubmissionStatus.html | 4 +- docs/reference/synGetSubmissions.html | 4 +- docs/reference/synGetTableColumns.html | 4 +- docs/reference/synGetTeam.html | 4 +- docs/reference/synGetTeamMembers.html | 4 +- docs/reference/synGetTeamOpenInvitations.html | 4 +- docs/reference/synGetUserProfile.html | 4 +- docs/reference/synGetWiki.html | 4 +- docs/reference/synGetWikiAttachments.html | 4 +- docs/reference/synGetWikiHeaders.html | 4 +- docs/reference/synInvalidateAPIKey.html | 4 +- docs/reference/synInviteToTeam.html | 4 +- docs/reference/synIsCertified.html | 4 +- docs/reference/synLogin.html | 4 +- docs/reference/synLogout.html | 4 +- docs/reference/synMd5Query.html | 4 +- docs/reference/synMove.html | 4 +- docs/reference/synOnweb.html | 4 +- docs/reference/synPrintEntity.html | 4 +- docs/reference/synRemoveFromDownloadList.html | 4 +- docs/reference/synRestDELETE.html | 4 +- docs/reference/synRestDeleteAsync.html | 4 +- docs/reference/synRestGET.html | 4 +- docs/reference/synRestGetAsync.html | 4 +- docs/reference/synRestPOST.html | 4 +- docs/reference/synRestPUT.html | 4 +- docs/reference/synRestPostAsync.html | 4 +- docs/reference/synRestPutAsync.html | 4 +- .../synSendMembershipInvitation.html | 4 +- docs/reference/synSendMessage.html | 4 +- docs/reference/synSetAnnotations.html | 4 +- docs/reference/synSetEndpoints.html | 4 +- docs/reference/synSetPermissions.html | 4 +- docs/reference/synSetProvenance.html | 4 +- docs/reference/synSetStorageLocation.html | 4 +- docs/reference/synStore.html | 4 +- docs/reference/synSubmit.html | 4 +- docs/reference/synTableQuery.html | 4 +- docs/reference/synUpdateActivity.html | 4 +- docs/reference/synUploadFileHandle.html | 4 +- docs/reference/synapser-package.html | 4 +- vignettes/docker.Rmd | 2 +- vignettes/installation.Rmd | 8 +- vignettes/synapser.Rmd | 4 +- 150 files changed, 428 insertions(+), 410 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ab3fa034..4f0fc56b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: synapser Type: Package Title: R Language Bindings for Synapse API -Version: 2.1.0 -Date: 2024-07-31 +Version: 2.1.1 +Date: 2024-08-20 Authors@R: c( person("Dan", "Lu", role = c("aut", "cre"), email = "dan.lu@sagebase.org"), person("Tom", "Yu", role = c("aut"), email = "thomas.yu@sagebase.org"), diff --git a/Dockerfile b/Dockerfile index 99e19067..7d9385d3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -9,4 +9,4 @@ RUN apt-get update && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* -RUN R -e "install.packages('synapser', repos=c('http://ran.synapse.org', 'http://cran.fhcrc.org'))" +RUN R -e "install.packages('synapser', repos=c('http://ran.synapse.org', 'https://cloud.r-project.org'))" diff --git a/Dockerfile.rstudio b/Dockerfile.rstudio index cbfb9cac..cf564718 100644 --- a/Dockerfile.rstudio +++ b/Dockerfile.rstudio @@ -13,6 +13,6 @@ RUN apt-get update && \ # Must install synapser as rstudio since we are relying on # the rstudio user to login USER rstudio -RUN R -e "install.packages('synapser', repos=c('http://ran.synapse.org', 'http://cran.fhcrc.org'))" +RUN R -e "install.packages('synapser', repos=c('http://ran.synapse.org', 'https://cloud.r-project.org'))" # when starting the container, it must run as root USER root diff --git a/NEWS.md b/NEWS.md index 9cf8b38c..36cea730 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +## synapser 2.1.1 + +### Improvements +* Pinned `rjson` package version to 0.2.21 to support R versions older than 4.4.0. + ## synapser 2.1.0 ### Improvements diff --git a/README.Rmd b/README.Rmd index bd2af733..ebdc5b43 100644 --- a/README.Rmd +++ b/README.Rmd @@ -47,13 +47,13 @@ adding the [Sage Bionetworks R Archive Network (RAN)](http://ran.synapse.org/) t repository list, e.g.: ```{r, eval=F} -install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) +install.packages("synapser", repos=c("http://ran.synapse.org", "https://cloud.r-project.org")) ``` Alternatively, edit your ~/.Rprofile and configure your default repositories: ```{r, eval=F} -options(repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) +options(repos=c("http://ran.synapse.org", "https://cloud.r-project.org")) ``` after which you may run install.packages without specifying the repositories: diff --git a/README.md b/README.md index 56318383..aded5ce1 100644 --- a/README.md +++ b/README.md @@ -38,14 +38,14 @@ repository list, e.g.: ```r -install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) +install.packages("synapser", repos=c("http://ran.synapse.org", "https://cloud.r-project.org")) ``` Alternatively, edit your ~/.Rprofile and configure your default repositories: ```r -options(repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) +options(repos=c("http://ran.synapse.org", "https://cloud.r-project.org")) ``` after which you may run install.packages without specifying the repositories: diff --git a/docs/404.html b/docs/404.html index c766b764..cf5d0dd2 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ synapser - 2.1.0 + 2.1.1 @@ -119,7 +119,7 @@

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