Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:08:15 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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: 2022-01-13 01:55:04 -0500 (Thu, 13 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: 2022-01-13 15:43:12 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 15:47:18 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 245.9 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 
  9.897   0.494  10.375 

Example timings

nanotatoR.Rcheck/nanotatoR-Ex.timings

nameusersystemelapsed
BNDBfrequency0.1380.0110.151
DGVfrequency0.0330.0020.035
Decipherfrequency0.0560.0020.059
FamilyInfoPrep0.0280.0030.032
OverlapRNAseq0.3140.0080.322
OverlapRNAseq_solo0.2420.0030.245
RNAseqcombine0.0010.0000.001
RNAseqcombine_solo0.2400.0030.244
SVexpression_duo_trio0.0000.0000.001
SVexpression_solo0.3260.0070.334
buildrunBNBedFiles0.0060.0010.006
clinvar_gene0.0240.0020.027
extract_clinvar_mod0.0260.0020.028
gene_extraction0.5800.0211.316
gene_list_generation0.4650.0131.774
gtr_gene0.0040.0010.005
internalFrequencyTrio_Duo0.2500.0040.256
internalFrequency_solo0.3540.0030.358
makeInternalBNDatabase0.0020.0010.002
mergingSMAP_SE0.0420.0030.046
mergingSMAP_SVMerge0.0160.0010.018
merging_SE_SVMerge0.0710.0060.077
nanotatoR0.0020.0010.002
nanotatoR_Duo_SVmerge0.0000.0010.001
nanotatoR_SVmerge_Trio0.0000.0000.001
nanotatoR_main_Duo_SE0.0000.0010.001
nanotatoR_main_Solo_SE1.0510.0411.094
nanotatoR_main_Solo_SVmerge0.2240.0070.232
nanotatoR_main_Trio_SE0.1260.0080.172
nonOverlapGenes0.0250.0020.026
nonOverlapRNAseq0.1950.0030.198
nonOverlapRNAseq_solo0.2410.0030.244
nonOverlappingDNGenes0.0420.0020.044
nonOverlappingUPGenes0.0430.0030.045
omim_gene0.0160.0010.454
overlapGenes0.0230.0020.025
overlapnearestgeneSearch0.0460.0030.050
overlappingGenes0.0430.0020.045
phenoextractHPO_mod0.0090.0010.009
readBNBedFiles0.0020.0000.004
readSMap0.0300.0070.037
readSMap_DLE0.0220.0040.026
reading_GTR0.0030.0010.003
reading_mim2gene0.0040.0010.004
run_bionano_filter_SE_Trio0.4580.0150.474
run_bionano_filter_SE_duo0.0000.0000.001
run_bionano_filter_SE_solo0.6910.0130.704
run_bionano_filter_SVMerge_Trio000
run_bionano_filter_SVMerge_duo0.0000.0010.001
run_bionano_filter_SVMerge_solo0.5560.0150.571