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This page was generated on 2024-02-18 02:28:54 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 1370/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nanotatoR 1.19.0  (landing page)
Surajit Bhattacharya
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/nanotatoR
git_branch: devel
git_last_commit: 12327ed
git_last_commit_date: 2023-10-24 11:13:33 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for nanotatoR on merida1


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: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2024-02-17 07:28:08 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 07:33:56 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 347.7 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/nanotatoR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nanotatoR/DESCRIPTION’ ... OK
* this is package ‘nanotatoR’ version ‘1.19.0’
* 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 ... 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-3.19-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/4.4-x86_64/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 10.861   0.673  12.276 

Example timings

nanotatoR.Rcheck/nanotatoR-Ex.timings

nameusersystemelapsed
BNDBfrequency0.1280.0310.167
DGVfrequency0.0540.0100.102
Decipherfrequency0.0660.0130.081
FamilyInfoPrep0.0340.0090.045
OverlapRNAseq0.3890.0390.449
OverlapRNAseq_solo0.3100.0140.338
RNAseqcombine0.0000.0010.001
RNAseqcombine_solo0.2640.0050.276
SVexpression_duo_trio0.0000.0010.002
SVexpression_solo0.3950.0140.436
buildrunBNBedFiles0.0080.0010.009
clinvar_gene0.0280.0030.032
extract_clinvar_mod0.0330.0030.044
gene_extraction1.1540.0702.056
gene_list_generation1.5530.0432.672
gtr_gene0.0050.0010.006
internalFrequencyTrio_Duo0.1980.0050.208
internalFrequency_solo0.3580.0040.368
makeInternalBNDatabase0.0020.0010.004
mergingSMAP_SE0.0480.0040.055
mergingSMAP_SVMerge0.0190.0020.021
merging_SE_SVMerge0.0860.0100.098
nanotatoR0.0020.0010.004
nanotatoR_Duo_SVmerge0.0010.0020.002
nanotatoR_SVmerge_Trio0.0000.0010.002
nanotatoR_main_Duo_SE0.0010.0010.002
nanotatoR_main_Solo_SE1.1880.1551.382
nanotatoR_main_Solo_SVmerge0.2780.0150.316
nanotatoR_main_Trio_SE0.1670.0120.193
nonOverlapGenes0.0420.0040.047
nonOverlapRNAseq0.2850.0070.307
nonOverlapRNAseq_solo0.2650.0070.296
nonOverlappingDNGenes0.0560.0040.068
nonOverlappingUPGenes0.0540.0030.061
omim_gene0.0220.0020.528
overlapGenes0.0260.0030.029
overlapnearestgeneSearch0.0650.0060.072
overlappingGenes0.0530.0030.060
phenoextractHPO_mod0.0100.0020.012
readBNBedFiles0.0050.0020.007
readSMap0.0330.0110.044
readSMap_DLE0.0240.0050.030
reading_GTR0.0040.0010.005
reading_mim2gene0.0050.0010.007
run_bionano_filter_SE_Trio0.5760.0330.642
run_bionano_filter_SE_duo0.0010.0010.001
run_bionano_filter_SE_solo0.8130.0280.902
run_bionano_filter_SVMerge_Trio0.0000.0010.001
run_bionano_filter_SVMerge_duo0.0000.0010.001
run_bionano_filter_SVMerge_solo0.6810.0280.757