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BioC 3.5: CHECK report for GenomicFeatures on malbec2

This page was generated on 2017-08-16 13:13:25 -0400 (Wed, 16 Aug 2017).

Package 539/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.28.4
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GenomicFeatures
Last Changed Rev: 130795 / Revision: 131943
Last Changed Date: 2017-06-30 04:30:46 -0400 (Fri, 30 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicFeatures
Version: 1.28.4
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.28.4.tar.gz
StartedAt: 2017-08-15 23:21:49 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:35:20 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 811.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicFeatures.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.28.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.28.4’
* 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 ... 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
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 ... NOTE
.writeMetadataFeatureTable: no visible global function definition for
  ‘packageDescription’
.write_metadata_table: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘exonicParts’ ‘intronicParts’
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 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 43.492  1.972  53.538
coverageByTranscript       24.908  6.556  31.511
makeFeatureDbFromUCSC      24.836  1.000 145.402
makeTxDbFromBiomart        15.616  0.264  74.099
extractTranscriptSeqs      12.052  0.024  13.665
makeTxDbFromUCSC            6.896  0.308 118.470
makeTxDbFromGFF             5.948  0.024   6.068
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.5-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/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.0880.0000.087
TxDb-class1.5440.0441.785
as-format-methods2.3080.0042.314
coordinate-mapping-methods43.492 1.97253.538
coverageByTranscript24.908 6.55631.511
disjointExons000
extractTranscriptSeqs12.052 0.02413.665
extractUpstreamSeqs1.2200.0281.653
features0.0920.0000.096
getPromoterSeq-methods0.7600.0201.223
id2name0.1160.0080.125
makeFeatureDbFromUCSC 24.836 1.000145.402
makeTxDb1.2120.0121.223
makeTxDbFromBiomart15.616 0.26474.099
makeTxDbFromGFF5.9480.0246.068
makeTxDbFromGRanges2.2960.0042.308
makeTxDbFromUCSC 6.896 0.308118.470
makeTxDbPackage0.2840.0243.552
mapIdsToRanges0.7560.0440.804
mapRangesToIds0.5120.0040.513
microRNAs0.0000.0000.001
nearest-methods0.6040.0040.620
select-methods0.1600.0000.161
transcriptLengths4.1280.0364.165
transcriptLocs2refLocs3.7280.0204.591
transcripts1.7080.0081.715
transcriptsBy0.5480.0040.555
transcriptsByOverlaps0.2680.0000.268