* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/dataone.Rcheck’
* using R Under development (unstable) (2025-02-14 r87716)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘dataone/DESCRIPTION’ ... OK
* this is package ‘dataone’ version ‘2.2.2’
* package encoding: UTF-8
* 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 whether package ‘dataone’ can be installed ... [19s/25s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/dataone-00install.html' for details.
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [22s/27s] OK
* checking Rd files ... 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 ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [14s/24s] OK
  Running ‘testthat.R’ [13s/23s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [40s/52s] OK
* checking PDF version of manual ... [12s/16s] OK
* checking HTML version of manual ... [6s/10s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE