Back to Build/check report for BioC 3.14 annotations
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This page was generated on 2022-01-19 06:00:08 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for synaptome.db on nebbiolo2


To the developers/maintainers of the synaptome.db package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 33/33HostnameOS / ArchINSTALLBUILDCHECK
synaptome.db 0.99.8  (landing page)
Oksana Sorokina
Snapshot Date: 2022-01-19 02:30:01 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/synaptome.db
git_branch: master
git_last_commit: b8ca355
git_last_commit_date: 2021-10-06 07:15:35 -0500 (Wed, 06 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: synaptome.db
Version: 0.99.8
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:synaptome.db.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings synaptome.db_0.99.8.tar.gz
StartedAt: 2022-01-19 03:02:56 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 03:05:17 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 141.1 seconds
RetCode: 0
Status:   OK  
CheckDir: synaptome.db.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:synaptome.db.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings synaptome.db_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-annotation/meat/synaptome.db.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synaptome.db/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synaptome.db’ version ‘0.99.8’
* 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 R 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 ... OK
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

synaptome.db.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL synaptome.db
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘synaptome.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: synaptome.db
snapshotDate(): 2022-01-07
loading from cache
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-01-07
loading from cache
** testing if installed package can be loaded from final location
snapshotDate(): 2022-01-07
loading from cache
** testing if installed package keeps a record of temporary installation path
* DONE (synaptome.db)

Tests output

synaptome.db.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
snapshotDate(): 2022-01-07
loading from cache
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 36 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  8.131   0.330   8.937 

Example timings

synaptome.db.Rcheck/synaptome.db-Ex.timings

nameusersystemelapsed
findGenesByEntrez0.0810.0000.081
findGenesByName0.0770.0000.077
getAllGenes4BrainRegion0.1060.0040.111
getAllGenes4Compartment0.1070.0040.112
getBrainRegions0.0090.0000.009
getCompartments0.0090.0000.008
getGeneDiseaseByEntres0.0780.0000.077
getGeneDiseaseByIDs0.1140.0040.117
getGeneDiseaseByName0.0850.0000.085
getGeneIdByEntrez0.0480.0000.048
getGeneIdByName0.0340.0000.034
getGeneInfoByEntrez0.2070.0000.206
getGeneInfoByIDs0.0380.0000.038
getGeneInfoByName0.1390.0000.139
getGenes4BrainRegion0.0430.0000.044
getGenes4Compartment0.0850.0000.085
getGenesByID0.0430.0000.044
getIGraphFromPPI0.1230.0000.124
getPPIbyEntrez0.0730.0000.073
getPPIbyIDs0.0720.0000.073
getPPIbyIDs4BrainRegion0.1870.0000.186
getPPIbyIDs4Compartment0.2930.0040.297
getPPIbyName0.0670.0000.068
getTableFromPPI0.1250.0040.130