Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for R453Plus1Toolbox on zin1

This page was generated on 2016-09-21 03:37:06 -0700 (Wed, 21 Sep 2016).

Package 964/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.23.0
Hans-Ulrich Klein
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: R453Plus1Toolbox
Version: 1.23.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.23.0.tar.gz
StartedAt: 2016-09-20 11:09:03 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:13:12 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 249.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.23.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘R453Plus1Toolbox’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.annotateVariants_MapperSet: no visible binding for global variable
  ‘Hsapiens’
.ava2vcf: no visible binding for global variable ‘Hsapiens’
.baseQualityHist: no visible global function definition for ‘hist’
.complexity.dust: no visible global function definition for ‘hist’
.complexity.dust: no visible global function definition for ‘abline’
.complexity.entropy: no visible global function definition for ‘hist’
.complexity.entropy: no visible global function definition for ‘abline’
.detectBreakpoints: no visible binding for global variable ‘Hsapiens’
.dinucleotideOddsRatio: no visible global function definition for
  ‘abline’
.gcContentHist: no visible global function definition for ‘hist’
.getEnsemblInfo: no visible binding for global variable ‘cds_length’
.getEnsemblInfo: no visible binding for global variable
  ‘ensembl_transcript_id’
.getMutations: no visible binding for global variable ‘PatternStart’
.getMutations: no visible binding for global variable ‘PatternEnd’
.htmlReport: no visible binding for global variable ‘VarFreqForward’
.htmlReport: no visible binding for global variable ‘VarFreqReverse’
.plotVariants: no visible binding for global variable ‘mutation’
.readLengthHist: no visible global function definition for ‘hist’
.sequenceQualityHist: no visible global function definition for ‘hist’
.sequenceQualityHist_sr: no visible global function definition for
  ‘hist’
qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’
qualityReportSFF: no visible global function definition for ‘Sweave’
annotateVariants,MapperSet-BSgenome: no visible binding for global
  variable ‘Hsapiens’
annotateVariants,MapperSet-missing: no visible binding for global
  variable ‘Hsapiens’
ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’
baseQualityHist,QualityScaledDNAStringSet: no visible global function
  definition for ‘hist’
complexity.dust,DNAStringSet: no visible global function definition for
  ‘hist’
complexity.dust,DNAStringSet: no visible global function definition for
  ‘abline’
complexity.entropy,DNAStringSet: no visible global function definition
  for ‘hist’
complexity.entropy,DNAStringSet: no visible global function definition
  for ‘abline’
detectBreakpoints,list: no visible binding for global variable
  ‘Hsapiens’
dinucleotideOddsRatio,DNAStringSet: no visible global function
  definition for ‘abline’
gcContentHist,DNAStringSet: no visible global function definition for
  ‘hist’
plotVariants,AnnotatedVariants-character: no visible global function
  definition for ‘rainbow’
plotVariants,data.frame-character: no visible global function
  definition for ‘rainbow’
readLengthHist,DNAStringSet: no visible global function definition for
  ‘hist’
sequenceQualityHist,QualityScaledDNAStringSet: no visible global
  function definition for ‘hist’
sequenceQualityHist,ShortReadQ: no visible global function definition
  for ‘hist’
subset,AVASet: no visible binding for global variable ‘referenceSeqID’
Undefined global functions or variables:
  Hsapiens PatternEnd PatternStart Sweave VarFreqForward VarFreqReverse
  abline cds_length ensembl_transcript_id hist mutation rainbow
  referenceSeqID
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "hist")
  importFrom("utils", "Sweave")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AVASet,ANY,ANY,ANY'
  generic '[' and siglist 'Breakpoints,ANY,ANY,ANY'
  generic '[' and siglist 'SFFContainer,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’
for details.


R453Plus1Toolbox.Rcheck/00install.out:

* installing *source* package ‘R453Plus1Toolbox’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readSFF.c -o readSFF.o
readSFF.c: In function ‘readSFF’:
readSFF.c:46:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(buffer, fileLen, 1, file);
   ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.2080.0080.216
AVASet0.1040.0000.105
AnnotatedVariants-class0.0000.0040.002
MapperSet-class0.0240.0040.026
MapperSet0.0040.0000.006
SFFContainer-class0.0000.0000.001
SFFRead-class0.0040.0000.001
alignShortReads1.7600.0001.865
annotateVariants0.0000.0000.002
assayDataAmp0.0040.0000.005
ava2vcf0.1720.0000.170
avaSetExample0.0120.0000.013
avaSetFiltered0.0200.0000.018
avaSetFiltered_annot0.0040.0000.002
breakpoints0.0000.0000.003
calculateTiTv0.0080.0000.010
captureArray0.0040.0000.002
coverageOnTarget0.1080.0040.110
demultiplexReads0.0680.0040.074
detectBreakpoints0.3800.0360.423
fDataAmp0.0120.0000.014
featureDataAmp0.0120.0000.014
filterChimericReads1.5520.0001.550
genomeSequencerMIDs0.0160.0000.017
getAlignedReads0.0720.0000.072
getVariantPercentages0.0320.0000.033
htmlReport3.2440.0563.323
mapperSetExample0.0040.0000.005
mergeBreakpoints3.6200.2604.095
mutationInfo0.0040.0000.003
plotAmpliconCoverage000
plotChimericReads2.1760.0042.181
plotVariants0.0040.0000.004
plotVariationFrequency0.0000.0000.001
qualityReportSFF000
readSFF0.0560.0000.056
readsOnTarget0.2120.0000.211
referenceSequences0.0080.0000.007
regions0.0040.0000.003
removeLinker0.0200.0000.018
sequenceCaptureLinkers0.0040.0000.004
setVariantFilter0.0520.0040.057
variants0.0000.0000.003
writeSFF0.0200.0000.024