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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:synaptome.db.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings synaptome.db_0.99.16.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-annotation/meat/synaptome.db.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘synaptome.db/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synaptome.db’ version ‘0.99.16’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘synaptome.db’ can be installed ... OK
* checking installed package size ... OK
* 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 whether startup messages can be suppressed ... NOTE
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BioNAR’
* 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) findGeneByCompartmentPaperCnt.Rd:28: Lost braces; missing escapes or markup?
    28 | Other {Gene functions}: 
       |       ^
checkRd: (-1) findGeneByPaperCnt.Rd:28: Lost braces; missing escapes or markup?
    28 | Other {Gene functions}: 
       |       ^
checkRd: (-1) findGeneByPapers.Rd:33: Lost braces; missing escapes or markup?
    33 | Other {Gene functions}: 
       |       ^
checkRd: (-1) findGenesByEntrez.Rd:36: Lost braces; missing escapes or markup?
    36 | Other {Lookup functions}: 
       |       ^
checkRd: (-1) findGenesByEntrez.Rd:39: Lost braces; missing escapes or markup?
    39 | Other {Gene functions}: 
       |       ^
checkRd: (-1) findGenesByName.Rd:34: Lost braces; missing escapes or markup?
    34 | Other {Lookup functions}: 
       |       ^
checkRd: (-1) findGenesByName.Rd:37: Lost braces; missing escapes or markup?
    37 | Other {Gene functions}: 
       |       ^
checkRd: (-1) getAllGenes4BrainRegion.Rd:44: Lost braces; missing escapes or markup?
    44 | Other {BrainRegion functions}: 
       |       ^
checkRd: (-1) getAllGenes4BrainRegion.Rd:49: Lost braces; missing escapes or markup?
    49 | Other {BrainRegion Gene functions}: 
       |       ^
checkRd: (-1) getAllGenes4Compartment.Rd:25: Lost braces; missing escapes or markup?
    25 | Other {Gene functions}: 
       |       ^
checkRd: (-1) getAllGenes4Compartment.Rd:34: Lost braces; missing escapes or markup?
    34 | Other {Compartment functions}: 
       |       ^
checkRd: (-1) getBrainRegions.Rd:27: Lost braces; missing escapes or markup?
    27 | Other {BrainRegion functions}: 
       |       ^
checkRd: (-1) getCompartments.Rd:21: Lost braces; missing escapes or markup?
    21 | Other {Compartment functions}: 
       |       ^
checkRd: (-1) getGeneDiseaseByEntres.Rd:30: Lost braces; missing escapes or markup?
    30 | Other {Disease functions}: 
       |       ^
checkRd: (-1) getGeneDiseaseByIDs.Rd:30: Lost braces; missing escapes or markup?
    30 | Other {Disease functions}: 
       |       ^
checkRd: (-1) getGeneDiseaseByName.Rd:24: Lost braces; missing escapes or markup?
    24 | Other {Disease functions}: 
       |       ^
checkRd: (-1) getGeneInfoByEntrez.Rd:39: Lost braces; missing escapes or markup?
    39 | Other {GeneInfo functions}: 
       |       ^
checkRd: (-1) getGeneInfoByIDs.Rd:50: Lost braces; missing escapes or markup?
    50 | Other {GeneInfo functions}: 
       |       ^
checkRd: (-1) getGeneInfoByName.Rd:54: Lost braces; missing escapes or markup?
    54 | Other {GeneInfo functions}: 
       |       ^
checkRd: (-1) getGeneInfoByPapers.Rd:58: Lost braces; missing escapes or markup?
    58 | Other {GeneInfo functions}: 
       |       ^
checkRd: (-1) getGenes4BrainRegion.Rd:49: Lost braces; missing escapes or markup?
    49 | Other {BrainRegion functions}: 
       |       ^
checkRd: (-1) getGenes4BrainRegion.Rd:54: Lost braces; missing escapes or markup?
    54 | Other {BrainRegion Gene functions}: 
       |       ^
checkRd: (-1) getGenes4Compartment.Rd:34: Lost braces; missing escapes or markup?
    34 | Other {Gene functions}: 
       |       ^
checkRd: (-1) getGenes4Compartment.Rd:43: Lost braces; missing escapes or markup?
    43 | Other {Compartment functions}: 
       |       ^
checkRd: (-1) getGenesByID.Rd:33: Lost braces; missing escapes or markup?
    33 | Other {Gene functions}: 
       |       ^
checkRd: (-1) getIGraphFromPPI.Rd:40: Lost braces; missing escapes or markup?
    40 | Other {PPI functions}: 
       |       ^
checkRd: (-1) getMutations4DiseaseByEntres.Rd:31: Lost braces; missing escapes or markup?
    31 | Other {Mutation functions}: 
       |       ^
checkRd: (-1) getMutations4DiseaseByIDs.Rd:54: Lost braces; missing escapes or markup?
    54 | Other {Mutation functions}: 
       |       ^
checkRd: (-1) getMutations4DiseaseByName.Rd:33: Lost braces; missing escapes or markup?
    33 | Other {Mutation functions}: 
       |       ^
checkRd: (-1) getPPIbyEntrez.Rd:42: Lost braces; missing escapes or markup?
    42 | Other {PPI functions}: 
       |       ^
checkRd: (-1) getPPIbyIDs.Rd:42: Lost braces; missing escapes or markup?
    42 | Other {PPI functions}: 
       |       ^
checkRd: (-1) getPPIbyIDs4BrainRegion.Rd:56: Lost braces; missing escapes or markup?
    56 | Other {PPI functions}: 
       |       ^
checkRd: (-1) getPPIbyIDs4BrainRegion.Rd:64: Lost braces; missing escapes or markup?
    64 | Other {BrainRegion functions}: 
       |       ^
checkRd: (-1) getPPIbyIDs4Compartment.Rd:39: Lost braces; missing escapes or markup?
    39 | Other {PPI functions}: 
       |       ^
checkRd: (-1) getPPIbyIDs4Compartment.Rd:47: Lost braces; missing escapes or markup?
    47 | Other {Compartment functions}: 
       |       ^
checkRd: (-1) getPPIbyName.Rd:44: Lost braces; missing escapes or markup?
    44 | Other {PPI functions}: 
       |       ^
checkRd: (-1) getTableFromPPI.Rd:44: Lost braces; missing escapes or markup?
    44 | Other {PPI functions}: 
       |       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getIGraphFromPPI.Rd: igraph
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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘synaptome.db-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graphFromSynaptomeByEntrez
> ### Title: Utility function to create network from 'synaptome.db' data
> ### Aliases: graphFromSynaptomeByEntrez
> 
> ### ** Examples
> 
> library(synaptome.db)
> cid<-match('Presynaptic', getCompartments()$Name)
> geneTable<-getAllGenes4Compartment(cid)
> gg<-graphFromSynaptomeByEntrez(geneTable$HumanEntrez)
Execution halted
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-annotation/meat/synaptome.db.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL synaptome.db
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘synaptome.db’ ...
** this is package ‘synaptome.db’ version ‘0.99.16’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: synaptome.db
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** testing if installed package can be loaded from final location
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** testing if installed package keeps a record of temporary installation path
* DONE (synaptome.db)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> test_check("synaptome.db")
Loading required package: synaptome.db
Loading required package: synaptome.data
Loading required package: AnnotationHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
 10.599   0.890  11.481