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CHECK report for customProDB on malbec1

This page was generated on 2021-05-06 12:27:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the customProDB package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 411/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.30.1  (landing page)
Xiaojing Wang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/customProDB
Branch: RELEASE_3_12
Last Commit: 2c66727
Last Changed Date: 2021-04-26 13:05:49 -0400 (Mon, 26 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: customProDB
Version: 1.30.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings customProDB_1.30.1.tar.gz
StartedAt: 2021-05-06 00:35:20 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:41:19 -0400 (Thu, 06 May 2021)
EllapsedTime: 358.5 seconds
RetCode: 0
Status:   OK  
CheckDir: customProDB.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings customProDB_1.30.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/customProDB.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.30.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘customProDB’ 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
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Bed2Range: no visible binding for global variable ‘V5’
OutputNovelJun: no visible binding for global variable ‘jun_type’
OutputVarproseq: no visible binding for global variable ‘genename’
OutputVarproseq: no visible binding for global variable ‘txname’
OutputVarproseq: no visible binding for global variable ‘proname’
OutputVarproseq: no visible binding for global variable ‘aaref’
OutputVarproseq: no visible binding for global variable ‘aapos’
OutputVarproseq: no visible binding for global variable ‘aavar’
OutputVarproseq: no visible binding for global variable ‘rsid’
OutputVarproseq_single: no visible binding for global variable
  ‘genename’
OutputVarproseq_single: no visible binding for global variable ‘txname’
OutputVarproseq_single: no visible binding for global variable
  ‘proname’
OutputVarproseq_single: no visible binding for global variable ‘aaref’
OutputVarproseq_single: no visible binding for global variable ‘aapos’
OutputVarproseq_single: no visible binding for global variable ‘aavar’
OutputVarproseq_single: no visible binding for global variable ‘rsid’
Outputaberrant: no visible binding for global variable ‘pro_name’
Positionincoding: no visible binding for global variable ‘cds_start’
Positionincoding: no visible binding for global variable ‘cds_end’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘ensembl_gene_id’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘pro_name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘chrom’
PrepareAnnotationEnsembl: no visible binding for global variable ‘name’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationEnsembl: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible binding for global variable ‘name’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘mrnaAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘protAcc’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘transcript’
PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleleCount’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘alleles’
PrepareAnnotationRefseq: no visible binding for global variable
  ‘COSMIC’
Varlocation: no visible binding for global variable ‘pro_name’
Undefined global functions or variables:
  COSMIC V5 aapos aaref aavar alleleCount alleles cds_end cds_start
  chrom ensembl_gene_id genename jun_type mrnaAcc name pro_name proname
  protAcc rsid transcript txname
* 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
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
PrepareAnnotationEnsembl 12.308  0.108  28.157
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/customProDB.Rcheck/00check.log’
for details.



Installation output

customProDB.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL customProDB
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘customProDB’ ...
** 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 (customProDB)

Tests output


Example timings

customProDB.Rcheck/customProDB-Ex.timings

nameusersystemelapsed
Bed2Range0.1520.0080.180
InputVcf1.0200.0681.087
JunctionType1.1400.0241.186
Multiple_VCF1.8080.0201.830
OutputNovelJun2.0440.1042.149
OutputVarprocodingseq0.6280.0160.644
OutputVarproseq0.9480.0080.954
OutputVarproseq_single0.9360.0160.952
Outputaberrant0.5120.0040.516
Outputproseq0.8120.0080.840
OutputsharedPro2.6840.0082.727
Positionincoding0.4720.0000.476
PrepareAnnotationEnsembl12.308 0.10828.157
PrepareAnnotationRefseq0.0040.0000.000
SharedJunc0.9200.0000.921
Varlocation000
aaVariation0.6280.0000.629
calculateRPKM0.9240.0080.936
easyRun2.0520.0042.056
easyRun_mul4.2600.0044.275