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BioC 3.0: CHECK report for GenomicFeatures on perceval

This page was generated on 2015-04-10 09:54:42 -0700 (Fri, 10 Apr 2015).

Package 367/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.18.7
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GenomicFeatures
Last Changed Rev: 102060 / Revision: 102249
Last Changed Date: 2015-04-07 14:45:31 -0700 (Tue, 07 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: GenomicFeatures
Version: 1.18.7
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.18.7.tar.gz
StartedAt: 2015-04-10 01:59:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:11:41 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 706.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicFeatures.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.18.7.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.18.7’
* 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 ... [32s/46s] 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
'library' or 'require' calls in package code:
  ‘FDb.UCSC.tRNAs’ ‘mirbase.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘biomaRt:::martBM’
  ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘rtracklayer:::ucscTableOutputs’ ‘S4Vectors:::duplicatedIntegerQuads’
  ‘S4Vectors:::fancy_mseq’ ‘S4Vectors:::matchIntegerQuads’
  ‘S4Vectors:::orderIntegerQuads’ ‘S4Vectors:::V_recycle’
  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
.extract_and_combine: no visible global function definition for
  ‘getSeq’
.extractTranscriptSeqsFromOneSeq: no visible global function definition
  for ‘getSeq’
.microRNAs: no visible global function definition for ‘mirbase_dbconn’
supportedMiRBaseBuildValues: no visible global function definition for
  ‘toTable’
supportedMiRBaseBuildValues: no visible binding for global variable
  ‘mirbaseSPECIES’
getPromoterSeq,GRanges: no visible global function definition for
  ‘getSeq’
getPromoterSeq,GRangesList: no visible global function definition for
  ‘getSeq’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [83s/220s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                              user system elapsed
extractTranscriptSeqs       15.946  0.151  17.578
transcriptLocs2refLocs      12.106  0.262  12.423
extractUpstreamSeqs          8.292  0.623   9.852
makeTranscriptDbFromBiomart  7.100  0.220  23.500
makeFeatureDbFromUCSC        6.020  0.272  90.621
makeTranscriptDbFromUCSC     3.565  0.153  37.271
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [142s/158s]
 [142s/158s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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_SEQS0.0010.0000.000
FeatureDb-class0.0330.0030.037
TxDb-class1.6710.1111.800
as-format-methods1.2210.0321.255
extractTranscriptSeqs15.946 0.15117.578
extractUpstreamSeqs8.2920.6239.852
features0.6350.0070.642
getPromoterSeq-methods1.4140.1942.007
id2name0.0580.0040.062
makeFeatureDbFromUCSC 6.020 0.27290.621
makeTranscriptDb0.0950.0050.101
makeTranscriptDbFromBiomart 7.10 0.2223.50
makeTranscriptDbFromGFF2.2510.0642.316
makeTranscriptDbFromUCSC 3.565 0.15337.271
makeTxDbPackage0.5200.0150.560
nearest-methods0.7230.0220.746
select-methods0.1660.0060.172
transcriptLocs2refLocs12.106 0.26212.423
transcripts2.1440.0582.202
transcriptsBy0.7080.0090.717
transcriptsByOverlaps0.2300.0030.233