Package: GenomicFeatures

Version: 1.30.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.30.3.tar.gz

StartedAt: 2018-04-12 04:17:42 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:32:53 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 911.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: GenomicFeatures.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.30.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.30.3’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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
':::' calls which should be '::':
  ‘S4Vectors:::duplicatedIntegerPairs’ ‘S4Vectors:::matchIntegerPairs’
  ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
  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 ... WARNING
Undocumented code objects:
  ‘makePackageName’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
coordinate-mapping-methods 41.717  2.259  48.038
coverageByTranscript       33.609  7.393  46.165
exonicParts                31.493  3.273  35.280
makeFeatureDbFromUCSC      31.516  1.720 154.697
makeTxDbFromBiomart        24.645  1.436 140.648
extractTranscriptSeqs      11.992  0.148  12.326
makeTxDbFromGFF             6.479  0.157   7.060
makeTxDbFromUCSC            5.943  0.171  40.154
transcriptLocs2refLocs      5.429  0.066   5.590
transcriptLengths           5.346  0.145   5.590
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  
  Error in BiocGenerics:::testPackage("GenomicFeatures") : 
    unit tests failed for package GenomicFeatures
  Calls: <Anonymous> -> <Anonymous>
  In addition: Warning messages:
  1: In .get_cds_IDX(type, phase) :
    The "phase" metadata column contains non-NA values for features of type
    exon. This information was ignored.
  2: In .get_cds_IDX(type, phase) :
    The "phase" metadata column contains non-NA values for features of type
    stop_codon. This information was ignored.
  3: In .get_cds_IDX(type, phase) :
    The "phase" metadata column contains non-NA values for features of type
    stop_codon. This information was ignored.
  Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicFeatures)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

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

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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
Timing stopped at: 8.893 0.237 26.5
Error in checkIdentical(TARGET_NEXONS_PER_TX, as.integer(nexons_per_tx)) : 
  FALSE 
 
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
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
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... 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 Apr 12 04:32:47 2018 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 1 failure
FAILURE in test_makeTxDbFromBiomart: Error in checkIdentical(TARGET_NEXONS_PER_TX, as.integer(nexons_per_tx)) : 
  FALSE 
 

Test files with failing tests

   test_makeTxDbFromBiomart.R 
     test_makeTxDbFromBiomart 


Error in BiocGenerics:::testPackage("GenomicFeatures") : 
  unit tests failed for package GenomicFeatures
Calls: <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
2: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
3: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
Execution halted

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.001	0.000	0.001
FeatureDb-class	0.096	0.014	0.111
TxDb-class	0.985	0.022	1.041
as-format-methods	2.331	0.013	2.404
coordinate-mapping-methods	41.717	2.259	48.038
coverageByTranscript	33.609	7.393	46.165
disjointExons	0.000	0.001	0.000
exonicParts	31.493	3.273	35.280
extractTranscriptSeqs	11.992	0.148	12.326
extractUpstreamSeqs	1.433	0.196	1.848
features	0.049	0.002	0.051
getPromoterSeq-methods	0.527	0.019	0.547
id2name	0.203	0.006	0.209
makeFeatureDbFromUCSC	31.516	1.720	154.697
makeTxDb	1.723	0.063	1.847
makeTxDbFromBiomart	24.645	1.436	140.648
makeTxDbFromEnsembl	0.662	0.011	2.321
makeTxDbFromGFF	6.479	0.157	7.060
makeTxDbFromGRanges	3.360	0.011	3.434
makeTxDbFromUCSC	5.943	0.171	40.154
makeTxDbPackage	0.479	0.022	3.111
mapIdsToRanges	0.682	0.002	0.704
mapRangesToIds	0.792	0.002	0.802
microRNAs	0.000	0.000	0.001
nearest-methods	0.474	0.006	0.499
select-methods	0.376	0.006	0.395
transcriptLengths	5.346	0.145	5.590
transcriptLocs2refLocs	5.429	0.066	5.590
transcripts	2.250	0.016	2.298
transcriptsBy	0.975	0.008	0.993
transcriptsByOverlaps	0.360	0.002	0.365