Multiple platform build/check report for BioC 3.14 - CHECK results for GenomicFeatures on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: GenomicFeatures

Version: 1.46.5

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_1.46.5.tar.gz

StartedAt: 2022-04-12 20:13:50 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:47:02 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 1991.7 seconds

RetCode: 0

Status: OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

##############################################################################
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###
### 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_1.46.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.46.5'
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      79.43  10.53  126.25
makeTxDbFromBiomart        78.63   3.39  235.25
exonicParts                43.02   2.35   45.36
coverageByTranscript       28.22   4.44   32.65
extractTranscriptSeqs      12.55   0.34   13.00
coordinate-mapping-methods 12.42   0.21   13.49
makeTxDbFromUCSC           11.02   0.18   39.16
transcriptLocs2refLocs      9.42   1.12   41.85
makeTxDbFromGFF             8.00   0.03   13.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      73.70   1.80  117.61
makeTxDbFromBiomart        61.44   0.75  149.02
coordinate-mapping-methods 57.11   2.62  301.67
exonicParts                41.46   2.05   43.51
coverageByTranscript       20.81   3.81   24.71
extractTranscriptSeqs      13.73   0.31   14.05
makeTxDbFromUCSC           10.59   0.10   49.73
makeTxDbFromGFF             9.70   0.03    9.93
transcriptLocs2refLocs      8.45   0.88    9.34
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenomicFeatures_1.46.5.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_1.46.5.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.46.5.zip && rm GenomicFeatures_1.46.5.tar.gz GenomicFeatures_1.46.5.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
  7 1132k    7 91587    0     0   468k      0  0:00:02 --:--:--  0:00:02  468k
100 1132k  100 1132k    0     0  1318k      0 --:--:-- --:--:-- --:--:-- 1318k

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_1.46.5.zip
* DONE (GenomicFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 20:43:59 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 
 145.42    5.34  178.68


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ... 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
Error in x$.self$finalize() : attempt to apply non-function
In addition: 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.
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
'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 -- Tue Apr 12 20:46:51 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 (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
2: In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
> 
> proc.time()
   user  system elapsed 
 144.96    2.21  172.10

name	user	system	elapsed
FeatureDb-class	0.04	0.00	0.05
TxDb-class	0.56	0.22	0.78
as-format-methods	1.59	0.36	1.95
coordinate-mapping-methods	12.42	0.21	13.49
coverageByTranscript	28.22	4.44	32.65
exonicParts	43.02	2.35	45.36
extractTranscriptSeqs	12.55	0.34	13.00
extractUpstreamSeqs	1.72	0.03	1.75
features	0.06	0.00	0.06
getPromoterSeq-methods	0.64	0.02	0.66
id2name	0.17	0.00	0.17
makeFeatureDbFromUCSC	79.43	10.53	126.25
makeTxDb	0.09	0.00	0.09
makeTxDbFromBiomart	78.63	3.39	235.25
makeTxDbFromEnsembl	0	0	0
makeTxDbFromGFF	8.00	0.03	13.67
makeTxDbFromGRanges	3.76	0.05	3.91
makeTxDbFromUCSC	11.02	0.18	39.16
makeTxDbPackage	0.42	0.02	3.29
mapIdsToRanges	0.94	0.00	0.94
mapRangesToIds	0.78	0.00	0.78
microRNAs	0	0	0
nearest-methods	0.71	0.01	0.72
select-methods	0.2	0.0	0.2
transcriptLengths	4.62	0.07	4.69
transcriptLocs2refLocs	9.42	1.12	41.85
transcripts	2.89	0.03	2.92
transcriptsBy	0.91	0.03	0.93
transcriptsByOverlaps	0.20	0.00	0.21

name	user	system	elapsed
FeatureDb-class	0.06	0.00	0.07
TxDb-class	1.33	0.03	1.35
as-format-methods	1.73	0.02	1.75
coordinate-mapping-methods	57.11	2.62	301.67
coverageByTranscript	20.81	3.81	24.71
exonicParts	41.46	2.05	43.51
extractTranscriptSeqs	13.73	0.31	14.05
extractUpstreamSeqs	1.39	0.06	1.45
features	0.06	0.00	0.06
getPromoterSeq-methods	0.53	0.00	0.53
id2name	0.21	0.00	0.21
makeFeatureDbFromUCSC	73.70	1.80	117.61
makeTxDb	0.07	0.00	0.08
makeTxDbFromBiomart	61.44	0.75	149.02
makeTxDbFromEnsembl	0	0	0
makeTxDbFromGFF	9.70	0.03	9.93
makeTxDbFromGRanges	3.1	0.0	3.1
makeTxDbFromUCSC	10.59	0.10	49.73
makeTxDbPackage	0.79	0.01	4.97
mapIdsToRanges	0.80	0.02	0.81
mapRangesToIds	0.78	0.00	0.78
microRNAs	0	0	0
nearest-methods	0.72	0.01	0.73
select-methods	0.20	0.00	0.21
transcriptLengths	3.82	0.05	3.86
transcriptLocs2refLocs	8.45	0.88	9.34
transcripts	3.20	0.03	3.23
transcriptsBy	1.09	0.00	1.09
transcriptsByOverlaps	0.22	0.01	0.24

CHECK results for GenomicFeatures on tokay2

Summary

Command output

Installation output

Tests output

Example timings