Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-20 11:07:51 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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 riesling1


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 1262/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nanotatoR 1.11.0  (landing page)
Surajit Bhattacharya
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/nanotatoR
git_branch: master
git_last_commit: e57fa17
git_last_commit_date: 2021-10-26 12:51:40 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: nanotatoR
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nanotatoR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings nanotatoR_1.11.0.tar.gz
StartedAt: 2022-01-19 19:31:28 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 19:33:49 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 141.6 seconds
RetCode: 0
Status:   OK  
CheckDir: nanotatoR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nanotatoR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings nanotatoR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/nanotatoR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nanotatoR/DESCRIPTION' ... OK
* this is package 'nanotatoR' version '1.11.0'
* 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 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
  'D:/biocbuild/bbs-3.15-bioc/meat/nanotatoR.Rcheck/00check.log'
for details.



Installation output

nanotatoR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL nanotatoR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'nanotatoR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nanotatoR'
    finding HTML links ... done
    BNDBfrequency                           html  
    DGVfrequency                            html  
    Decipherfrequency                       html  
    FamilyInfoPrep                          html  
    OverlapRNAseq                           html  
    OverlapRNAseq_solo                      html  
    RNAseqcombine                           html  
    RNAseqcombine_solo                      html  
    SVexpression_duo_trio                   html  
    SVexpression_solo                       html  
    buildrunBNBedFiles                      html  
    clinvar_gene                            html  
    extract_clinvar_mod                     html  
    gene_extraction                         html  
    gene_list_generation                    html  
    gtr_gene                                html  
    internalFrequencyTrio_Duo               html  
    internalFrequency_solo                  html  
    makeInternalBNDatabase                  html  
    mergingSMAP_SE                          html  
    mergingSMAP_SVMerge                     html  
    merging_SE_SVMerge                      html  
    nanotatoR                               html  
    nanotatoR_Duo_SVmerge                   html  
    nanotatoR_SVmerge_Trio                  html  
    nanotatoR_main_Duo_SE                   html  
    nanotatoR_main_Solo_SE                  html  
    nanotatoR_main_Solo_SVmerge             html  
    nanotatoR_main_Trio_SE                  html  
    nonOverlapGenes                         html  
    nonOverlapRNAseq                        html  
    nonOverlapRNAseq_solo                   html  
    nonOverlappingDNGenes                   html  
    nonOverlappingUPGenes                   html  
    omim_gene                               html  
    overlapGenes                            html  
    overlapnearestgeneSearch                html  
    overlappingGenes                        html  
    phenoextractHPO_mod                     html  
    readBNBedFiles                          html  
    readSMap                                html  
    readSMap_DLE                            html  
    reading_GTR                             html  
    reading_mim2gene                        html  
    run_bionano_filter_SE_Trio              html  
    run_bionano_filter_SE_duo               html  
    run_bionano_filter_SE_solo              html  
    run_bionano_filter_SVMerge_Trio         html  
    run_bionano_filter_SVMerge_duo          html  
    run_bionano_filter_SVMerge_solo         html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MicrobiotaProcess' is missing or broken
 done

Tests output

nanotatoR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   5.18    0.50    5.67 

Example timings

nanotatoR.Rcheck/nanotatoR-Ex.timings

nameusersystemelapsed
BNDBfrequency0.040.000.04
DGVfrequency0.020.000.02
Decipherfrequency0.010.000.01
FamilyInfoPrep000
OverlapRNAseq0.150.000.14
OverlapRNAseq_solo0.090.000.09
RNAseqcombine000
RNAseqcombine_solo0.090.020.11
SVexpression_duo_trio000
SVexpression_solo0.130.010.14
buildrunBNBedFiles000
clinvar_gene0.010.000.02
extract_clinvar_mod0.020.000.01
gene_extraction0.370.021.04
gene_list_generation0.220.001.25
gtr_gene000
internalFrequencyTrio_Duo0.160.000.15
internalFrequency_solo0.120.000.13
makeInternalBNDatabase000
mergingSMAP_SE0.020.000.01
mergingSMAP_SVMerge0.000.010.02
merging_SE_SVMerge0.020.020.03
nanotatoR000
nanotatoR_Duo_SVmerge000
nanotatoR_SVmerge_Trio000
nanotatoR_main_Duo_SE000
nanotatoR_main_Solo_SE0.320.060.42
nanotatoR_main_Solo_SVmerge0.080.000.08
nanotatoR_main_Trio_SE0.050.000.05
nonOverlapGenes0.010.000.01
nonOverlapRNAseq0.10.00.1
nonOverlapRNAseq_solo0.080.000.07
nonOverlappingDNGenes0.010.020.04
nonOverlappingUPGenes0.020.000.01
omim_gene0.010.000.53
overlapGenes000
overlapnearestgeneSearch0.020.000.02
overlappingGenes0.000.010.01
phenoextractHPO_mod0.010.000.02
readBNBedFiles000
readSMap000
readSMap_DLE000
reading_GTR000
reading_mim2gene000
run_bionano_filter_SE_Trio0.140.030.18
run_bionano_filter_SE_duo000
run_bionano_filter_SE_solo0.270.000.26
run_bionano_filter_SVMerge_Trio000
run_bionano_filter_SVMerge_duo000
run_bionano_filter_SVMerge_solo0.180.000.22