Package: genbankr

Version: 1.6.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings genbankr_1.6.1.tar.gz

StartedAt: 2018-04-11 23:41:52 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:45:39 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 227.1 seconds

RetCode: 0

Status:  OK

CheckDir: genbankr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings genbankr_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/genbankr.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genbankr/DESCRIPTION’ ... OK
* this is package ‘genbankr’ version ‘1.6.1’
* 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 ‘genbankr’ 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

* installing *source* package ‘genbankr’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genbankr)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> BiocGenerics:::testPackage("genbankr")
Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
No exons read from genbank file. Assuming sections of CDS are full exons
No transcript features (mRNA) found, using spans of CDSs
No exons read from genbank file. Assuming sections of CDS are full exons
No exons read from genbank file. Assuming sections of CDS are full exons
No exons read from genbank file. Assuming sections of CDS are full exons
No exons read from genbank file. Assuming sections of CDS are full exons
No exons read from genbank file. Assuming sections of CDS are full exons
No transcript features (mRNA) found, using spans of CDSs
No exons read from genbank file. Assuming sections of CDS are full exons
No transcript features (mRNA) found, using spans of CDSs
No exons read from genbank file. Assuming sections of CDS are full exons
No exons read from genbank file. Assuming sections of CDS are full exons
Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
No exons read from genbank file. Assuming sections of CDS are full exons
Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
No exons read from genbank file. Assuming sections of CDS are full exons
No transcript features (mRNA) found, using spans of CDSs


RUNIT TEST PROTOCOL -- Wed Apr 11 23:45:36 2018 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
genbankr RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In readLines(file) :
  incomplete final line found on '/home/biocbuild/bbs-3.6-bioc/meat/genbankr.Rcheck/genbankr/unitTests/compjoin.gbk'
2: In fill_stack_df(rawvars, sqinfo = sqinfo) :
  Got unexpected multi-value field(s) [ note ]. The resulting column(s) will be of class CharacterList, rather than vector(s). Please contact the maintainer if multi-valuedness is expected/meaningful for the listed field(s).
3: In fill_stack_df(rawvars, sqinfo = sqinfo) :
  Got unexpected multi-value field(s) [ note ]. The resulting column(s) will be of class CharacterList, rather than vector(s). Please contact the maintainer if multi-valuedness is expected/meaningful for the listed field(s).
4: In make_feat_gr(str = rngstr, chr = chr, ats = c(type = type, attrs),  :
  Incomplete feature annotation detected. Omitting feature at <1..1353
5: In make_feat_gr(str = rngstr, chr = chr, ats = c(type = type, attrs),  :
  Incomplete feature annotation detected. Omitting feature at 689..>734
6: In make_feat_gr(str = rngstr, chr = chr, ats = c(type = type, attrs),  :
  Incomplete feature annotation detected. Omitting feature at 5..>660
7: In readLines(file) :
  incomplete final line found on '/home/biocbuild/bbs-3.6-bioc/meat/genbankr.Rcheck/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
 18.040   0.212  18.258 

name	user	system	elapsed
GBAccession	0.004	0.000	0.003
GenBank-classes	3.036	0.016	3.055
api-methods	2.608	0.008	2.622
gbk-api	1.596	0.004	1.601
gbkfile	1.604	0.004	1.617
intergenic	1.832	0.004	1.838
make_gbobjs	1.840	0.000	1.843
otherFeatures	1.324	0.040	1.363
parseGenBank	0.956	0.008	0.966
readGenBank	1.432	0.004	1.436
txdb	0.408	0.000	0.406
variants	1.572	0.000	1.572