Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-02 11:35:48 -0400 (Mon, 02 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 1357/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nanotatoR 1.16.0  (landing page)
Surajit Bhattacharya
Snapshot Date: 2023-10-01 14:00:12 -0400 (Sun, 01 Oct 2023)
git_url: https://git.bioconductor.org/packages/nanotatoR
git_branch: RELEASE_3_17
git_last_commit: 3b06cd8
git_last_commit_date: 2023-04-25 11:10:03 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for nanotatoR on nebbiolo1


To the developers/maintainers of the nanotatoR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: nanotatoR
Version: 1.16.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings nanotatoR_1.16.0.tar.gz
StartedAt: 2023-10-01 23:15:05 -0400 (Sun, 01 Oct 2023)
EndedAt: 2023-10-01 23:17:33 -0400 (Sun, 01 Oct 2023)
EllapsedTime: 147.8 seconds
RetCode: 0
Status:   OK  
CheckDir: nanotatoR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings nanotatoR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/nanotatoR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘nanotatoR/DESCRIPTION’ ... OK
* this is package ‘nanotatoR’ version ‘1.16.0’
* 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 loading without being on the library search path ... 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 ...
  ‘nanotatoR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/nanotatoR.Rcheck/00check.log’
for details.



Installation output

nanotatoR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL nanotatoR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
  5.035   0.206   5.230 

Example timings

nanotatoR.Rcheck/nanotatoR-Ex.timings

nameusersystemelapsed
BNDBfrequency0.0430.0160.060
DGVfrequency0.0140.0080.022
Decipherfrequency0.0120.0160.027
FamilyInfoPrep0.0110.0040.015
OverlapRNAseq0.1240.0280.152
OverlapRNAseq_solo0.0940.0150.110
RNAseqcombine000
RNAseqcombine_solo0.0980.0080.106
SVexpression_duo_trio000
SVexpression_solo0.1680.0120.180
buildrunBNBedFiles0.0030.0000.004
clinvar_gene0.0160.0000.017
extract_clinvar_mod0.0170.0000.018
gene_extraction0.5580.0401.259
gene_list_generation0.7300.0561.731
gtr_gene0.0030.0000.003
internalFrequencyTrio_Duo0.0920.0000.092
internalFrequency_solo0.1580.0040.162
makeInternalBNDatabase0.0010.0000.002
mergingSMAP_SE0.0190.0010.020
mergingSMAP_SVMerge0.0080.0000.007
merging_SE_SVMerge0.0300.0030.033
nanotatoR0.0020.0010.001
nanotatoR_Duo_SVmerge0.0010.0000.000
nanotatoR_SVmerge_Trio000
nanotatoR_main_Duo_SE0.0000.0000.001
nanotatoR_main_Solo_SE0.4260.0530.479
nanotatoR_main_Solo_SVmerge0.0910.0080.098
nanotatoR_main_Trio_SE0.0680.0040.072
nonOverlapGenes0.0090.0090.017
nonOverlapRNAseq0.1160.0120.129
nonOverlapRNAseq_solo0.1070.0040.111
nonOverlappingDNGenes0.0190.0040.023
nonOverlappingUPGenes0.0230.0000.023
omim_gene0.0140.0000.452
overlapGenes0.0050.0080.012
overlapnearestgeneSearch0.0270.0000.026
overlappingGenes0.0220.0000.022
phenoextractHPO_mod0.0050.0000.005
readBNBedFiles0.0000.0020.003
readSMap0.0080.0080.017
readSMap_DLE0.0070.0030.011
reading_GTR0.0020.0000.002
reading_mim2gene0.0020.0000.003
run_bionano_filter_SE_Trio0.1920.0320.225
run_bionano_filter_SE_duo000
run_bionano_filter_SE_solo0.3440.0110.356
run_bionano_filter_SVMerge_Trio0.0000.0010.001
run_bionano_filter_SVMerge_duo0.0000.0010.000
run_bionano_filter_SVMerge_solo0.2380.0060.244