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CHECK report for genbankr on tokay1

This page was generated on 2018-04-12 13:27:59 -0400 (Thu, 12 Apr 2018).

Package 529/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genbankr 1.6.1
Gabriel Becker
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/genbankr
Branch: RELEASE_3_6
Last Commit: b3ddec9
Last Changed Date: 2018-02-28 16:25:07 -0400 (Wed, 28 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genbankr
Version: 1.6.1
Command: rm -rf genbankr.buildbin-libdir genbankr.Rcheck && mkdir genbankr.buildbin-libdir genbankr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genbankr.buildbin-libdir genbankr_1.6.1.tar.gz >genbankr.Rcheck\00install.out 2>&1 && cp genbankr.Rcheck\00install.out genbankr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genbankr.buildbin-libdir --install="check:genbankr-install.out" --force-multiarch --no-vignettes --timings genbankr_1.6.1.tar.gz
StartedAt: 2018-04-12 00:10:39 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:16:42 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 363.0 seconds
RetCode: 0
Status:  OK  
CheckDir: genbankr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genbankr.buildbin-libdir genbankr.Rcheck && mkdir genbankr.buildbin-libdir genbankr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genbankr.buildbin-libdir genbankr_1.6.1.tar.gz >genbankr.Rcheck\00install.out 2>&1 && cp genbankr.Rcheck\00install.out genbankr-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genbankr.buildbin-libdir --install="check:genbankr-install.out" --force-multiarch --no-vignettes --timings genbankr_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genbankr.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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


install for i386

* installing *source* package 'genbankr' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'genbankr'
    finding HTML links ... done
    GBAccession                             html  
    GenBank-classes                         html  
    api-methods                             html  
    gbk-api                                 html  
    gbkfile                                 html  
    import                                  html  
    intergenic                              html  
    make_gbobjs                             html  
    otherFeatures                           html  
    parseGenBank                            html  
    readGenBank                             html  
    txdb                                    html  
    variants                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genbankr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genbankr' as genbankr_1.6.1.zip
* DONE (genbankr)
In R CMD INSTALL
In R CMD INSTALL

Tests output

genbankr.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 Apr 12 00:16:16 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genbankr.buildbin-libdir/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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genbankr.buildbin-libdir/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
  15.82    0.42   16.23

genbankr.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 Apr 12 00:16:37 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genbankr.buildbin-libdir/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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genbankr.buildbin-libdir/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
  20.57    0.29   20.89

Example timings

genbankr.Rcheck/examples_i386/genbankr-Ex.timings

nameusersystemelapsed
GBAccession000
GenBank-classes2.970.063.04
api-methods2.740.052.78
gbk-api1.340.031.38
gbkfile1.360.001.36
intergenic1.590.001.60
make_gbobjs1.360.001.36
otherFeatures1.360.001.35
parseGenBank1.040.001.05
readGenBank1.720.031.75
txdb0.380.000.38
variants1.470.001.47

genbankr.Rcheck/examples_x64/genbankr-Ex.timings

nameusersystemelapsed
GBAccession000
GenBank-classes3.780.013.80
api-methods2.740.032.77
gbk-api2.290.052.34
gbkfile1.640.001.64
intergenic1.770.001.77
make_gbobjs1.550.001.55
otherFeatures1.540.021.56
parseGenBank1.040.011.05
readGenBank1.540.001.54
txdb0.470.000.47
variants1.790.001.79