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This page was generated on 2021-09-24 15:06:41 -0400 (Fri, 24 Sep 2021).

CHECK results for genbankr on machv2

To the developers/maintainers of the genbankr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genbankr.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 706/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genbankr 1.20.0  (landing page)
Gabriel Becker
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/genbankr
git_branch: RELEASE_3_13
git_last_commit: 968c425
git_last_commit_date: 2021-05-19 12:19:55 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: genbankr
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2021-09-23 19:05:39 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 19:11:35 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 356.2 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/genbankr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genbankr/DESCRIPTION’ ... OK
* this is package ‘genbankr’ version ‘1.20.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/genbankr.Rcheck/00check.log’
for details.



Installation output

genbankr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genbankr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Thu Sep 23 19:11:28 2021 
*********************************************** 
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/4.1/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: This class is extending the deprecated RTLFile class from rtracklayer. Use BiocFile from BiocIO in place of RTLFile. 
7: In make_feat_gr(str = rngstr, chr = chr, ats = c(type = type, attrs),  :
  Incomplete feature annotation detected. Omitting feature at 5..>660
8: In readLines(file) :
  incomplete final line found on '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
 23.022   0.816  23.880 

Example timings

genbankr.Rcheck/genbankr-Ex.timings

nameusersystemelapsed
GBAccession0.0030.0000.003
GenBank-classes4.3590.1754.540
api-methods2.9530.0753.039
gbk-api2.4580.0092.470
gbkfile2.3160.0032.321
intergenic2.5580.0052.565
make_gbobjs2.4750.0062.485
otherFeatures2.3710.0132.389
parseGenBank1.2110.0031.215
readGenBank2.2920.0052.298
txdb1.1760.0041.182
variants2.4610.0102.474