Back to Multiple platform build/check report for BioC 3.10
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for customProDB on malbec1

This page was generated on 2020-04-15 12:07:46 -0400 (Wed, 15 Apr 2020).

Package 394/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.26.1
Xiaojing Wang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/customProDB
Branch: RELEASE_3_10
Last Commit: b8d27af
Last Changed Date: 2020-04-12 02:39:06 -0400 (Sun, 12 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: customProDB
Version: 1.26.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings customProDB_1.26.1.tar.gz
StartedAt: 2020-04-15 01:45:55 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:50:58 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 303.1 seconds
RetCode: 0
Status:  OK 
CheckDir: customProDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:customProDB.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings customProDB_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/customProDB.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.26.1’
* 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 or elapsed time > 5s
                          user system elapsed
PrepareAnnotationEnsembl 5.664  0.072  23.402
* 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-3.10-bioc/meat/customProDB.Rcheck/00check.log’
for details.



Installation output

customProDB.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL customProDB
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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
Bed2Range0.1320.0040.153
InputVcf0.8120.0841.131
JunctionType1.0000.0121.040
Multiple_VCF1.0520.0201.115
OutputNovelJun2.1960.0162.281
OutputVarprocodingseq1.6240.0041.666
OutputVarproseq0.5800.0040.584
OutputVarproseq_single0.6760.0040.689
Outputaberrant0.4200.0080.430
Outputproseq0.9440.0000.959
OutputsharedPro2.5360.0122.853
Positionincoding0.3960.0040.445
PrepareAnnotationEnsembl 5.664 0.07223.402
PrepareAnnotationRefseq000
SharedJunc0.7480.0000.792
Varlocation0.0000.0000.001
aaVariation0.7840.0040.786
calculateRPKM0.7920.0000.796
easyRun1.6600.0041.668
easyRun_mul4.3400.0004.342