Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:08:27 -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
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 machv2


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: 2022-01-18 01:55:07 -0500 (Tue, 18 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nanotatoR_1.10.0.tar.gz
StartedAt: 2022-01-18 15:42:44 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 15:46:50 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 246.3 seconds
RetCode: 0
Status:   OK  
CheckDir: nanotatoR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings nanotatoR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/nanotatoR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/nanotatoR.Rcheck/00check.log’
for details.



Installation output

nanotatoR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL nanotatoR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 
 10.006   0.495  10.851 

Example timings

nanotatoR.Rcheck/nanotatoR-Ex.timings

nameusersystemelapsed
BNDBfrequency0.1130.0110.125
DGVfrequency0.0480.0020.050
Decipherfrequency0.0500.0020.053
FamilyInfoPrep0.0210.0020.024
OverlapRNAseq0.2840.0060.291
OverlapRNAseq_solo0.2410.0040.245
RNAseqcombine000
RNAseqcombine_solo0.2210.0040.225
SVexpression_duo_trio0.0000.0010.001
SVexpression_solo0.3480.0090.358
buildrunBNBedFiles0.0050.0010.006
clinvar_gene0.0260.0010.028
extract_clinvar_mod0.0320.0020.033
gene_extraction0.6100.0211.229
gene_list_generation0.4580.0121.415
gtr_gene0.0040.0000.004
internalFrequencyTrio_Duo0.2600.0050.267
internalFrequency_solo0.3310.0030.336
makeInternalBNDatabase0.0020.0000.003
mergingSMAP_SE0.0430.0030.047
mergingSMAP_SVMerge0.0160.0010.018
merging_SE_SVMerge0.0730.0060.079
nanotatoR0.0020.0010.002
nanotatoR_Duo_SVmerge0.0000.0010.001
nanotatoR_SVmerge_Trio0.0000.0000.001
nanotatoR_main_Duo_SE0.0000.0010.002
nanotatoR_main_Solo_SE1.0510.0401.093
nanotatoR_main_Solo_SVmerge0.1960.0060.203
nanotatoR_main_Trio_SE0.1350.0060.141
nonOverlapGenes0.0300.0020.032
nonOverlapRNAseq0.2380.0070.250
nonOverlapRNAseq_solo0.2450.0030.248
nonOverlappingDNGenes0.0410.0020.042
nonOverlappingUPGenes0.0390.0020.041
omim_gene0.0190.0010.532
overlapGenes0.0210.0020.023
overlapnearestgeneSearch0.0540.0030.056
overlappingGenes0.0410.0020.043
phenoextractHPO_mod0.0080.0010.009
readBNBedFiles0.0030.0010.004
readSMap0.0290.0070.037
readSMap_DLE0.0200.0040.023
reading_GTR0.0030.0010.004
reading_mim2gene0.0040.0010.004
run_bionano_filter_SE_Trio0.4890.0160.507
run_bionano_filter_SE_duo0.0000.0010.001
run_bionano_filter_SE_solo0.7130.0150.727
run_bionano_filter_SVMerge_Trio0.0000.0000.001
run_bionano_filter_SVMerge_duo0.0000.0000.001
run_bionano_filter_SVMerge_solo0.5390.0130.562