Multiple platform build/check report for BioC 3.9 - CHECK report for genbankr on tokay2

Package: genbankr

Version: 1.11.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genbankr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings genbankr_1.11.0.tar.gz

StartedAt: 2019-04-09 02:54:03 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:00:00 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 357.3 seconds

RetCode: 0

Status: OK

CheckDir: genbankr.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genbankr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings genbankr_1.11.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/genbankr.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.11.0'
* 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 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
* 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 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 ...
** 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/genbankr_1.11.0.tar.gz && rm -rf genbankr.buildbin-libdir && mkdir genbankr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genbankr.buildbin-libdir genbankr_1.11.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL genbankr_1.11.0.zip && rm genbankr_1.11.0.tar.gz genbankr_1.11.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  348k  100  348k    0     0  5535k      0 --:--:-- --:--:-- --:--:-- 6221k

install for i386

* installing *source* package 'genbankr' ...
** R
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'genbankr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genbankr' as genbankr_1.11.0.zip
* DONE (genbankr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'genbankr' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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 -- Tue Apr 09 02:59:39 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 'C:/Users/biocbuild/bbs-3.9-bioc/R/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 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
  15.10    1.10   16.26


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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 -- Tue Apr 09 02:59:55 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 'C:/Users/biocbuild/bbs-3.9-bioc/R/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 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/genbankr/unitTests/compjoin.gbk'
> 
> proc.time()
   user  system elapsed 
  14.84    0.42   15.25

name	user	system	elapsed
GBAccession	0	0	0
GenBank-classes	2.37	0.70	3.21
api-methods	1.93	0.00	1.94
gbk-api	1.57	0.01	1.58
gbkfile	1.23	0.00	1.23
intergenic	2.09	0.00	2.10
make_gbobjs	1.64	0.00	1.64
otherFeatures	1.27	0.00	1.26
parseGenBank	0.84	0.00	0.85
readGenBank	1.61	0.00	1.61
txdb	0.58	0.00	0.62
variants	1.45	0.00	1.45

name	user	system	elapsed
GBAccession	0	0	0
GenBank-classes	1.92	0.06	1.98
api-methods	1.63	0.00	1.62
gbk-api	1.42	0.00	1.42
gbkfile	1.31	0.00	1.32
intergenic	1.33	0.00	1.32
make_gbobjs	1.2	0.0	1.2
otherFeatures	1.28	0.00	1.28
parseGenBank	0.83	0.00	0.83
readGenBank	1.25	0.02	1.27
txdb	0.36	0.00	0.36
variants	1.34	0.00	1.34

CHECK report for genbankr on tokay2

Summary

Command output

Installation output

Tests output

Example timings