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CHECK results for GenomicFeatures on tokay2


To the developers/maintainers of the GenomicFeatures package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFeatures.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 751/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.46.4  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenomicFeatures
git_branch: RELEASE_3_14
git_last_commit: d3ab6fd
git_last_commit_date: 2022-01-19 12:03:06 -0500 (Wed, 19 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  YES

Summary

Package: GenomicFeatures
Version: 1.46.4
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomicFeatures_1.46.4.tar.gz
StartedAt: 2022-01-20 20:25:17 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:53:19 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 1681.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomicFeatures.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomicFeatures_1.46.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.46.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicFeatures' 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 ... NOTE
':::' call which should be '::': 'rtracklayer:::tableNames'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  'rtracklayer:::resourceDescription'
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Missing link or links in documentation object 'as-format-methods.Rd':
  '[rtracklayer]{export}'

Missing link or links in documentation object 'makeTxDbFromGFF.Rd':
  '[rtracklayer]{import}'

Missing link or links in documentation object 'makeTxDbFromGRanges.Rd':
  '[rtracklayer]{import}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      90.81  18.41  151.06
makeTxDbFromBiomart        71.67   5.45  156.93
exonicParts                48.22   3.23   51.45
coverageByTranscript       30.14   4.07   34.21
extractTranscriptSeqs      15.08   0.24   15.42
coordinate-mapping-methods 12.06   0.36   14.23
transcriptLocs2refLocs     10.15   1.76   25.40
makeTxDbFromUCSC            9.84   0.12   34.41
makeTxDbFromGFF             8.33   0.00    8.43
transcriptLengths           4.57   0.60    5.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      76.34   2.35  129.53
makeTxDbFromBiomart        65.64   1.00  133.80
coordinate-mapping-methods 49.03   2.38   59.53
exonicParts                37.04   2.16   39.22
coverageByTranscript       20.94   4.12   25.08
makeTxDbFromUCSC           12.72   0.36   41.21
extractTranscriptSeqs      12.30   0.31   12.61
transcriptLocs2refLocs      8.19   0.95   16.24
makeTxDbFromGFF             8.66   0.03    8.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.



Installation output

GenomicFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenomicFeatures_1.46.4.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.46.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.46.4.zip && rm GenomicFeatures_1.46.4.tar.gz GenomicFeatures_1.46.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 28 1132k   28  325k    0     0  1263k      0 --:--:-- --:--:-- --:--:-- 1261k
100 1132k  100 1132k    0     0  3050k      0 --:--:-- --:--:-- --:--:-- 3053k

install for i386

* installing *source* package 'GenomicFeatures' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicFeatures'
    finding HTML links ... done
    FeatureDb-class                         html  
    finding level-2 HTML links ... done

    TxDb-class                              html  
    as-format-methods                       html  
    coordinate-mapping-methods              html  
    coverageByTranscript                    html  
    disjointExons                           html  
    exonicParts                             html  
    extractTranscriptSeqs                   html  
    extractUpstreamSeqs                     html  
    features                                html  
    getPromoterSeq-methods                  html  
    id2name                                 html  
    makeFeatureDbFromUCSC                   html  
    makeTxDb                                html  
    makeTxDbFromBiomart                     html  
    makeTxDbFromEnsembl                     html  
    makeTxDbFromGFF                         html  
    makeTxDbFromGRanges                     html  
    makeTxDbFromUCSC                        html  
    makeTxDbPackage                         html  
    mapIdsToRanges                          html  
    mapRangesToIds                          html  
    microRNAs                               html  
    nearest-methods                         html  
    select-methods                          html  
    transcriptLengths                       html  
    transcriptLocs2refLocs                  html  
    transcripts                             html  
    transcriptsBy                           html  
    transcriptsByOverlaps                   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 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.46.4.zip
* DONE (GenomicFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked

Tests output

GenomicFeatures.Rcheck/tests_i386/run_unitTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Thu Jan 20 20:50:01 2022 
*********************************************** 
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 73 test functions, 0 errors, 0 failures
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences a,
  b, and c. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences 1,
  2, 3, and 4. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
5: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
6: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
7: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
8: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
9: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
10: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
> 
> proc.time()
   user  system elapsed 
 142.67    4.71  180.31 

GenomicFeatures.Rcheck/tests_x64/run_unitTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... Ensembl site unresponsive, trying useast mirror
OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Thu Jan 20 20:53:08 2022 
*********************************************** 
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 73 test functions, 0 errors, 0 failures
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences a,
  b, and c. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences 1,
  2, 3, and 4. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
5: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
6: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
7: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
8: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
9: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
10: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
> 
> proc.time()
   user  system elapsed 
 146.57    2.26  186.65 

Example timings

GenomicFeatures.Rcheck/examples_i386/GenomicFeatures-Ex.timings

nameusersystemelapsed
FeatureDb-class0.050.000.05
TxDb-class0.640.120.76
as-format-methods1.500.371.88
coordinate-mapping-methods12.06 0.3614.23
coverageByTranscript30.14 4.0734.21
exonicParts48.22 3.2351.45
extractTranscriptSeqs15.08 0.2415.42
extractUpstreamSeqs1.770.101.87
features0.080.000.08
getPromoterSeq-methods0.640.020.66
id2name0.20.00.2
makeFeatureDbFromUCSC 90.81 18.41151.06
makeTxDb0.110.030.14
makeTxDbFromBiomart 71.67 5.45156.93
makeTxDbFromEnsembl000
makeTxDbFromGFF8.330.008.43
makeTxDbFromGRanges3.360.023.47
makeTxDbFromUCSC 9.84 0.1234.41
makeTxDbPackage0.390.002.87
mapIdsToRanges1.040.001.05
mapRangesToIds1.090.021.11
microRNAs000
nearest-methods0.720.000.72
select-methods0.150.040.20
transcriptLengths4.570.605.16
transcriptLocs2refLocs10.15 1.7625.40
transcripts2.830.022.85
transcriptsBy0.990.011.00
transcriptsByOverlaps0.210.000.22

GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings

nameusersystemelapsed
FeatureDb-class0.070.020.07
TxDb-class1.480.041.53
as-format-methods1.640.051.69
coordinate-mapping-methods49.03 2.3859.53
coverageByTranscript20.94 4.1225.08
exonicParts37.04 2.1639.22
extractTranscriptSeqs12.30 0.3112.61
extractUpstreamSeqs1.830.031.85
features0.080.000.08
getPromoterSeq-methods0.600.000.61
id2name0.210.000.21
makeFeatureDbFromUCSC 76.34 2.35129.53
makeTxDb0.480.010.50
makeTxDbFromBiomart 65.64 1.00133.80
makeTxDbFromEnsembl000
makeTxDbFromGFF8.660.038.69
makeTxDbFromGRanges3.820.003.92
makeTxDbFromUCSC12.72 0.3641.21
makeTxDbPackage0.410.002.83
mapIdsToRanges0.840.000.84
mapRangesToIds0.720.000.72
microRNAs000
nearest-methods0.620.000.63
select-methods0.180.000.17
transcriptLengths4.480.054.53
transcriptLocs2refLocs 8.19 0.9516.24
transcripts3.010.003.01
transcriptsBy0.970.020.99
transcriptsByOverlaps0.220.000.21