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CHECK report for genbankr on celaya2

This page was generated on 2019-04-09 13:16:08 -0400 (Tue, 09 Apr 2019).

Package 611/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genbankr 1.11.0
Gabriel Becker
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/genbankr
Branch: master
Last Commit: df55ef9
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: genbankr
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genbankr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genbankr_1.11.0.tar.gz
StartedAt: 2019-04-09 02:08:27 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:14:32 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 364.8 seconds
RetCode: 0
Status:  OK 
CheckDir: genbankr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genbankr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genbankr_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/genbankr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genbankr/DESCRIPTION’ ... OK
* this is package ‘genbankr’ version ‘1.11.0’
* 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 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 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


Installation output

genbankr.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genbankr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘genbankr’ ...
** 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 (genbankr)

Tests output

genbankr.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Tue Apr  9 02:14:25 2019 
*********************************************** 
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 '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/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 '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
 21.052   1.549  22.559 

Example timings

genbankr.Rcheck/genbankr-Ex.timings

nameusersystemelapsed
GBAccession0.0030.0010.004
GenBank-classes3.0940.2443.339
api-methods2.3450.0122.358
gbk-api2.1990.0072.206
gbkfile2.2490.0092.258
intergenic2.2940.0072.302
make_gbobjs2.0150.0082.023
otherFeatures2.2740.0062.280
parseGenBank1.4850.0031.488
readGenBank1.9340.0041.938
txdb0.7230.0050.731
variants2.2010.0062.208