##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodb_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodb.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodb/DESCRIPTION’ ... OK
* this is package ‘biodb’ version ‘1.15.0’
* 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 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 ... WARNING
Found the following significant warnings:
  closeMatchPpm.cpp:251:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/biodb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.0Mb
* 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 loading without being on the library search path ... 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 ...

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL biodb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘biodb’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c closeMatchPpm.cpp -o closeMatchPpm.o
closeMatchPpm.cpp: In function ‘Rcpp::List closeMatchPpm(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, double, double)’:
closeMatchPpm.cpp:251:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  251 |     free(pidxS);
      |     ~~~~^~~~~~~
closeMatchPpm.cpp:238:50: note: returned from ‘void* operator new [](std::size_t)’
  238 |     tIdxStruct *pidxS = new tIdxStruct[x.length()];
      |                                                  ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c test-100-ms_matching.cpp -o test-100-ms_matching.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/testthat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o biodb.so RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-biodb/00new/biodb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodb)