Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:28 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 nanotatoR on nebbiolo2


To the developers/maintainers of the nanotatoR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nanotatoR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1268/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nanotatoR 1.10.0  (landing page)
Surajit Bhattacharya
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/nanotatoR
git_branch: RELEASE_3_14
git_last_commit: 821a44d
git_last_commit_date: 2021-10-26 12:51:40 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: nanotatoR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings nanotatoR_1.10.0.tar.gz
StartedAt: 2022-01-20 08:36:38 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 08:39:06 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:   OK  
CheckDir: nanotatoR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings nanotatoR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/nanotatoR.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 ‘nanotatoR/DESCRIPTION’ ... OK
* this is package ‘nanotatoR’ version ‘1.10.0’
* 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:
  .travis.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 ‘nanotatoR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘GenomicRanges’
  All declared Imports should be used.
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/nanotatoR.Rcheck/00check.log’
for details.



Installation output

nanotatoR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL nanotatoR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘nanotatoR’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nanotatoR)

Tests output

nanotatoR.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)
> library(nanotatoR)

> 
> test_check("nanotatoR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  5.261   0.247   5.500 

Example timings

nanotatoR.Rcheck/nanotatoR-Ex.timings

nameusersystemelapsed
BNDBfrequency0.0480.0040.053
DGVfrequency0.0180.0000.017
Decipherfrequency0.0210.0000.021
FamilyInfoPrep0.0120.0000.012
OverlapRNAseq0.1750.0000.175
OverlapRNAseq_solo0.1180.0000.118
RNAseqcombine000
RNAseqcombine_solo0.1090.0030.113
SVexpression_duo_trio000
SVexpression_solo0.1890.0090.196
buildrunBNBedFiles0.0030.0020.006
clinvar_gene0.0200.0030.024
extract_clinvar_mod0.0190.0050.023
gene_extraction0.4160.0873.220
gene_list_generation0.3010.0131.228
gtr_gene0.0040.0000.004
internalFrequencyTrio_Duo0.1760.0200.196
internalFrequency_solo0.1740.0120.187
makeInternalBNDatabase0.0010.0000.001
mergingSMAP_SE0.0190.0000.019
mergingSMAP_SVMerge0.0050.0040.008
merging_SE_SVMerge0.0310.0040.035
nanotatoR0.0000.0000.001
nanotatoR_Duo_SVmerge0.0000.0000.001
nanotatoR_SVmerge_Trio0.0010.0000.000
nanotatoR_main_Duo_SE000
nanotatoR_main_Solo_SE0.4660.1040.571
nanotatoR_main_Solo_SVmerge0.0930.0000.093
nanotatoR_main_Trio_SE0.060.000.06
nonOverlapGenes0.0150.0000.015
nonOverlapRNAseq0.1310.0000.131
nonOverlapRNAseq_solo0.1480.0040.152
nonOverlappingDNGenes0.020.000.02
nonOverlappingUPGenes0.0190.0000.019
omim_gene0.0190.0000.444
overlapGenes0.0160.0000.016
overlapnearestgeneSearch0.0310.0030.035
overlappingGenes0.0280.0000.028
phenoextractHPO_mod0.0070.0000.007
readBNBedFiles0.0030.0000.004
readSMap0.0200.0000.021
readSMap_DLE0.0160.0000.016
reading_GTR0.0040.0000.004
reading_mim2gene0.0030.0000.003
run_bionano_filter_SE_Trio0.1910.0080.199
run_bionano_filter_SE_duo0.0010.0000.000
run_bionano_filter_SE_solo0.3370.0000.337
run_bionano_filter_SVMerge_Trio0.0000.0000.001
run_bionano_filter_SVMerge_duo000
run_bionano_filter_SVMerge_solo0.2390.0000.240