############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodb_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodb.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodb/DESCRIPTION’ ... OK * this is package ‘biodb’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .gitlab-ci.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodb’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package 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 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 ... OK * checking Rd files ... NOTE checkRd: (-1) BiodbMain.Rd:101: Lost braces 101 | Closes \\code{BiodbMain} instance. Call this method when you are done with | ^ checkRd: (-1) BiodbMain.Rd:102: Lost braces 102 | your \\code{BiodbMain} instance. | ^ checkRd: (-1) BiodbMain.Rd:124: Lost braces 124 | \\code{BiodbMain} (databases, fields or configuration keys).} | ^ checkRd: (-1) BiodbMain.Rd:138: Lost braces 138 | Returns the single instance of the \\code{BiodbConfig} class. | ^ checkRd: (-1) BiodbMain.Rd:144: Lost braces 144 | The instance of the \\code{BiodbConfig} class attached to | ^ checkRd: (-1) BiodbMain.Rd:166: Lost braces 166 | Returns the single instance of the \\code{BiodbDbsInfo} class. | ^ checkRd: (-1) BiodbMain.Rd:172: Lost braces 172 | The instance of the \\code{BiodbDbsInfo} class attached to | ^ checkRd: (-1) BiodbMain.Rd:180: Lost braces 180 | Returns the single instance of the \\code{BiodbEntryFields} class. | ^ checkRd: (-1) BiodbMain.Rd:186: Lost braces 186 | The instance of the \\code{BiodbEntryFields} class | ^ checkRd: (-1) BiodbMain.Rd:194: Lost braces 194 | Returns the single instance of the \\code{BiodbFactory} class. | ^ checkRd: (-1) BiodbMain.Rd:200: Lost braces 200 | The instance of the \\code{BiodbFactory} class attached to | ^ checkRd: (-1) BiodbMain.Rd:208: Lost braces 208 | Returns the single instance of the \\code{BiodbRequestScheduler} | ^ checkRd: (-1) BiodbMain.Rd:215: Lost braces 215 | The instance of the \\code{BiodbRequestScheduler} class | ^ checkRd: (-1) BiodbMain.Rd:291: Lost braces 291 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances.} | ^ checkRd: (-1) BiodbMain.Rd:295: Lost braces 295 | \item{\code{flatten}}{If set to \\code{TRUE} and the field has a cardinality | ^ checkRd: (-1) BiodbMain.Rd:299: Lost braces 299 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will be | ^ checkRd: (-1) BiodbMain.Rd:312: Lost braces 312 | \\code{TRUE}, otherwise a list. | ^ checkRd: (-1) BiodbMain.Rd:320: Lost braces 320 | (\\code{BiodbEntry} objects) into a data frame. | ^ checkRd: (-1) BiodbMain.Rd:341: Lost braces 341 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances or a list of list of | ^ checkRd: (-1) BiodbMain.Rd:342: Lost braces 342 | \\code{BiodbEntry} instances.} | ^ checkRd: (-1) BiodbMain.Rd:344: Lost braces 344 | \item{\code{only.atomic}}{If set to \\code{TRUE}, output only atomic fields, i.e.: | ^ checkRd: (-1) BiodbMain.Rd:348: Lost braces 348 | \item{\code{null.to.na}}{If set to \\code{TRUE}, each \\code{NULL} entry in the | ^ checkRd: (-1) BiodbMain.Rd:348: Lost braces 348 | \item{\code{null.to.na}}{If set to \\code{TRUE}, each \\code{NULL} entry in the | ^ checkRd: (-1) BiodbMain.Rd:351: Lost braces 351 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will be output.} | ^ checkRd: (-1) BiodbMain.Rd:360: Lost braces 360 | \item{\code{drop}}{If set to \\code{TRUE} and the resulting data frame has only one | ^ checkRd: (-1) BiodbMain.Rd:365: Lost braces 365 | \item{\code{flatten}}{If set to \\code{TRUE}, then each field with a cardinality | ^ checkRd: (-1) BiodbMain.Rd:467: Lost braces 467 | Converts a list of \\code{BiodbEntry} objects into JSON. Returns a vector of | ^ checkRd: (-1) BiodbMain.Rd:476: Lost braces 476 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances. It may contain NULL | ^ checkRd: (-1) BiodbMain.Rd:479: Lost braces 479 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will added to JSON | ^ checkRd: (-1) BiodbMain.Rd:595: Lost braces 595 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances. It may contain NULL | ^ checkRd: (-1) BiodbMain.Rd:617: Lost braces 617 | \item{\code{entries}}{A list of \\code{BiodbEntry} instances. It may contain NULL | ^ checkRd: (-1) BiodbMain.Rd:623: Lost braces 623 | \item{\code{compute}}{If set to \\code{TRUE}, computable fields will be saved too.} | ^ checkRd: (-1) BiodbMain.Rd:649: Lost braces 649 | \\code{NULL}, copy the whole database.} | ^ checkRd: (-1) BiodbMain.Rd:675: Lost braces 675 | method is \\code{BiodbEntryField :isVector()}." | ^ checkRd: (-1) BiodbPersistentCache.Rd:120: Lost braces 120 | \item{\code{conn}}{If not \\code{NULL}, checks if the cache system is readable for | ^ checkRd: (-1) BiodbPersistentCache.Rd:126: Lost braces 126 | \\code{TRUE} if the cache system is readable, | ^ checkRd: (-1) BiodbPersistentCache.Rd:127: Lost braces 127 | \\code{FALSE} otherwise. | ^ checkRd: (-1) BiodbPersistentCache.Rd:142: Lost braces 142 | \item{\code{conn}}{If not \\code{NULL}, checks if the cache system is writable for | ^ checkRd: (-1) BiodbPersistentCache.Rd:148: Lost braces 148 | \\code{TRUE} if the cache system is writable, | ^ checkRd: (-1) BiodbPersistentCache.Rd:149: Lost braces 149 | \\code{FALSE} otherwise. | ^ checkRd: (-1) BiodbPersistentCache.Rd:230: Lost braces 230 | A character vector, the same size as \\code{names}, | ^ checkRd: (-1) BiodbPersistentCache.Rd:276: Lost braces 276 | A logical vector, the same size as \\code{name}, with \\code{TRUE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:276: Lost braces 276 | A logical vector, the same size as \\code{name}, with \\code{TRUE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:277: Lost braces 277 | value if the file exists in the cache, or \\code{FALSE} otherwise. | ^ checkRd: (-1) BiodbPersistentCache.Rd:302: Lost braces 302 | A logical vector, the same size as \\code{name}, with \\code{TRUE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:302: Lost braces 302 | A logical vector, the same size as \\code{name}, with \\code{TRUE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:303: Lost braces 303 | value if the file exists in the cache, or \\code{FALSE} otherwise. | ^ checkRd: (-1) BiodbPersistentCache.Rd:325: Lost braces 325 | A logical vector, the same size as \\code{name}, with | ^ checkRd: (-1) BiodbPersistentCache.Rd:326: Lost braces 326 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:326: Lost braces 326 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:351: Lost braces 351 | A logical vector, the same size as \\code{name}, with | ^ checkRd: (-1) BiodbPersistentCache.Rd:352: Lost braces 352 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:352: Lost braces 352 | \\code{TRUE} value if the marker file exists in the cache, or \\code{FALSE} | ^ checkRd: (-1) BiodbPersistentCache.Rd:428: Lost braces 428 | \item{\code{output.vector}}{If set to \\code{TRUE}, force output to be a | ^ checkRd: (-1) BiodbPersistentCache.Rd:429: Lost braces 429 | \\code{vector} instead of a \\code{list}. Where the list contains a | ^ checkRd: (-1) BiodbPersistentCache.Rd:429: Lost braces 429 | \\code{vector} instead of a \\code{list}. Where the list contains a | ^ checkRd: (-1) BiodbPersistentCache.Rd:430: Lost braces 430 | \\code{NULL}, the \\code{vector} will contain an \\code{NA} value.} | ^ checkRd: (-1) BiodbPersistentCache.Rd:430: Lost braces 430 | \\code{NULL}, the \\code{vector} will contain an \\code{NA} value.} | ^ checkRd: (-1) BiodbPersistentCache.Rd:430: Lost braces 430 | \\code{NULL}, the \\code{vector} will contain an \\code{NA} value.} | ^ checkRd: (-1) BiodbPersistentCache.Rd:435: Lost braces 435 | A list (or a vector if \\code{output.vector} is set to | ^ checkRd: (-1) BiodbPersistentCache.Rd:436: Lost braces 436 | \\code{TRUE}), the same size as \\code{name}, containing the contents of the | ^ checkRd: (-1) BiodbPersistentCache.Rd:436: Lost braces 436 | \\code{TRUE}), the same size as \\code{name}, containing the contents of the | ^ checkRd: (-1) BiodbPersistentCache.Rd:437: Lost braces 437 | files. If some file does not exist, a \\code{NULL} value is inserted inside | ^ checkRd: (-1) BiodbPersistentCache.Rd:454: Lost braces 454 | files. It must have the same length as \\code{name}.} | ^ checkRd: (-1) BiodbPersistentCache.Rd:667: Lost braces 667 | \item{\code{extract.name}}{If set to \\code{TRUE}, instead of returning the file | ^ checkRd: (-1) BiodbPersistentCache.Rd:671: Lost braces 671 | \item{\code{full.path}}{If set to \\code{TRUE}, returns full path for files.} | ^ checkRd: (-1) BiodbPersistentCache.Rd:677: Lost braces 677 | \\code{extract.name} is set to \\code{TRUE}. | ^ checkRd: (-1) BiodbPersistentCache.Rd:677: Lost braces 677 | \\code{extract.name} is set to \\code{TRUE}. | ^ checkRd: (-1) BiodbPersistentCache.Rd:695: Lost braces 695 | \\code{BiodbConfig :isEnabled('cache.system')}. | ^ checkRd: (-1) BiodbPersistentCache.Rd:706: Lost braces 706 | \\code{BiodbConfig :enable('cache.system')}. | ^ checkRd: (-1) BiodbPersistentCache.Rd:717: Lost braces 717 | \\code{BiodbConfig :disable('cache.system')}. | ^ * checking Rd metadata ... 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodb.Rcheck/00check.log’ for details.