| Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:33:21 -0400 (Thu, 12 Apr 2018).
| Package 564/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFeatures 1.30.3 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| 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.
GenomicFeatures.Rcheck/00install.out
* 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)
GenomicFeatures.Rcheck/tests/run_unitTests.Rout.fail
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
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
| 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 | |