Package: GenomicFeatures

Version: 1.35.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicFeatures_1.35.9.tar.gz

StartedAt: 2019-04-09 02:14:28 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:34:46 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 1217.8 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 --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenomicFeatures_1.35.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.35.9’
* 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 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
coordinate-mapping-methods 136.918  7.053 145.546
exonicParts                 72.200  9.065  82.234
coverageByTranscript        50.690 20.945  72.137
makeFeatureDbFromUCSC       64.507  4.366 136.608
makeTxDbFromBiomart         59.529  3.674 170.075
extractTranscriptSeqs       19.016  0.405  19.440
makeTxDbFromGFF             13.274  0.179  13.632
transcriptLocs2refLocs      10.640  0.208  10.852
makeTxDbFromGRanges          6.673  0.052   6.740
transcriptLengths            6.363  0.288   6.650
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenomicFeatures
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GenomicFeatures’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (GenomicFeatures)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, 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, 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 ... 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.
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: 27.22 0.797 45.42
Error in checkTrue(GenomicFeatures:::compareTxDbs(target_txdb, current_txdb)) : 
  Test not TRUE

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
'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  9 02:34:36 2019 
*********************************************** 
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 checkTrue(GenomicFeatures:::compareTxDbs(target_txdb, current_txdb)) : 
  Test not TRUE


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	0.000	0.000	0.001
FeatureDb-class	0.093	0.005	0.100
TxDb-class	1.159	0.182	1.347
as-format-methods	2.197	0.284	2.552
coordinate-mapping-methods	136.918	7.053	145.546
coverageByTranscript	50.690	20.945	72.137
disjointExons	0	0	0
exonicParts	72.200	9.065	82.234
extractTranscriptSeqs	19.016	0.405	19.440
extractUpstreamSeqs	2.829	0.899	4.443
features	0.089	0.003	0.094
getPromoterSeq-methods	1.086	0.062	1.149
id2name	0.318	0.007	0.325
makeFeatureDbFromUCSC	64.507	4.366	136.608
makeTxDb	0.185	0.007	0.200
makeTxDbFromBiomart	59.529	3.674	170.075
makeTxDbFromEnsembl	0.001	0.001	0.001
makeTxDbFromGFF	13.274	0.179	13.632
makeTxDbFromGRanges	6.673	0.052	6.740
makeTxDbFromUCSC	0.001	0.001	0.002
makeTxDbPackage	0.398	0.016	3.865
mapIdsToRanges	0.650	0.003	0.653
mapRangesToIds	0.987	0.008	0.995
microRNAs	0.000	0.000	0.001
nearest-methods	2.347	0.052	2.398
select-methods	0.336	0.008	0.346
transcriptLengths	6.363	0.288	6.650
transcriptLocs2refLocs	10.640	0.208	10.852
transcripts	4.149	0.038	4.187
transcriptsBy	0.987	0.015	1.002
transcriptsByOverlaps	0.271	0.005	0.276