• using R Under development (unstable) (2025-07-06 r88390)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b1)     Debian flang-new version 19.1.7 (3+b1)
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘dataone/DESCRIPTION’ ... OK
• this is package ‘dataone’ version ‘2.2.2’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘dataone’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/3s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [16s/24s] OK
• checking Rd files ... [1s/2s] NOTE checkRd: (-1) AuthenticationManager-class.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) AuthenticationManager-class.Rd:61: Lost braces     61 | \code{\link{dataone}}{ package description.}        | ^ checkRd: (-1) CNode-class.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) CNode-class.Rd:42: Lost braces     42 | \code{\link{dataone}}{ package description.}        | ^ checkRd: (-1) CNode.Rd:36: Lost braces     36 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) CertificateManager-class.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) CertificateManager-class.Rd:75: Lost braces     75 | \code{\link{dataone}}{ package description.}        | ^ checkRd: (-1) D1Client-class.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Client-class.Rd:41: Lost braces     41 | \code{\link{dataone}}{ package description.}        | ^ checkRd: (-1) D1Client-initialize.Rd:37: Lost braces     37 | \code{\link[=D1Client-class]{dataone}}{ class description.}        | ^ checkRd: (-1) D1Client.Rd:48: Lost braces     48 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) D1Node-class.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Node-class.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) D1Object-class.Rd:31: Lost braces     31 | \code{\link{dataone}}{ package description.}        | ^ checkRd: (-1) D1Object-initialize.Rd:25: Lost braces     25 | \code{\link[=D1Object-class]{D1Object}}{ class description.}        | ^ checkRd: (-1) D1Object.Rd:19: Lost braces     19 | \code{\link[=D1Object-class]{D1Object}}{ class description.}        | ^ checkRd: (-1) MNode-class.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) MNode-class.Rd:73: Lost braces     73 | \code{\link{dataone}}{ package description.}        | ^ checkRd: (-1) MNode.Rd:37: Lost braces     37 | \code{\link[=MNode-class]{MNode}}{ class description.}        | ^ checkRd: (-1) archive.Rd:69: Lost braces     69 | \code{\link[=D1Node-class]{D1Node}}{ class description.}        | ^ checkRd: (-1) convert.csv.Rd:33: Lost braces     33 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) createDataPackage.Rd:49: Lost braces     49 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) d1IdentifierSearch.Rd:34: Lost braces     34 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) d1SolrQuery.Rd:39: Lost braces     39 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) dataone-defunct.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-defunct.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone-deprecated.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) dataone.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) downloadObject.Rd:51: Lost braces     51 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) encodeUrlPath.Rd:34: Lost braces     34 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) encodeUrlQuery.Rd:34: Lost braces     34 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getCN.Rd:28: Lost braces     28 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getChecksum.Rd:48: Lost braces     48 | \code{\link{D1Node-class}{D1Node}}{ class description.}        | ^ checkRd: (-1) getD1Object.Rd:35: Lost braces     35 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getDataObject.Rd:77: Lost braces     77 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getDataPackage.Rd:70: Lost braces     70 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getEndpoint.Rd:33: Lost braces     33 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getFormat.Rd:36: Lost braces     36 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) getMN.Rd:35: Lost braces     35 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getMNode.Rd:37: Lost braces     37 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) getMNodeId.Rd:29: Lost braces     29 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) getObject.Rd:45: Lost braces     45 | \code{\link{D1Node-class}{D1Node}}{ class description.}        | ^ checkRd: (-1) getPackage.Rd:52: Lost braces     52 | \code{\link[=MNode-class]{MNode}}{ class description.}        | ^ checkRd: (-1) getSystemMetadata.Rd:57: Lost braces     57 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) hasReservation.Rd:46: Lost braces     46 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) isAuthorized.Rd:50: Lost braces     50 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) listFormats.Rd:32: Lost braces     32 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) listMemberNodes.Rd:26: Lost braces     26 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) listNodes.Rd:33: Lost braces     33 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) reserveIdentifier.Rd:43: Lost braces     43 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) setMNodeId.Rd:27: Lost braces     27 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) setObsoletedBy.Rd:33: Lost braces     33 | \code{\link[=CNode-class]{CNode}}{ class description.}        | ^ checkRd: (-1) setPublicAccess.Rd:24: Lost braces     24 | \code{\link[=DataObject-class]{DataObject}}{ class description.}        | ^ checkRd: (-1) uploadDataObject.Rd:61: Lost braces     61 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^ checkRd: (-1) uploadDataPackage.Rd:88: Lost braces     88 | \code{\link[=D1Client-class]{D1Client}}{ class description.}        | ^
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   dataone-defunct.Rd: getData, getIdentifier, getFormatId,     setPublicAccess, canRead, addData   setPublicAccess.Rd: DataObject-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/8s] OK   Running ‘testthat.R’ [5s/8s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [16s/24s] OK
• checking PDF version of manual ... [8s/10s] OK
• checking HTML version of manual ... [4s/8s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 NOTEs