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BioC 3.2: CHECK report for RIPSeeker on windows1.bioconductor.org

This page was generated on 2015-10-27 17:30:12 -0400 (Tue, 27 Oct 2015).

Package 886/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.10.0
Yue Li
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RIPSeeker
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RIPSeeker
Version: 1.10.0
Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.10.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.10.0.tar.gz
StartedAt: 2015-10-27 05:06:42 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:11:46 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 304.1 seconds
RetCode: 0
Status:  OK  
CheckDir: RIPSeeker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.10.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'IRanges' 'GenomicRanges' 'SummarizedExperiment' 'Rsamtools'
  'GenomicAlignments' 'rtracklayer'
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 whether package 'RIPSeeker' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' call to 'Rsamtools' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'ChIPpeakAnno' 'GenomicFeatures' 'biomaRt' 'parallel'
  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
addPseudoAlignment: no visible global function definition for 'Rle'
annotateRIP: no visible global function definition for 'getAnnotation'
annotateRIP: no visible global function definition for 'getBM'
binCount: no visible global function definition for 'runValue'
binCount: no visible global function definition for 'seqlengths'
combineRIP: no visible global function definition for 'seqlengths<-'
combineRIP: no visible global function definition for 'seqlengths'
computeRPKM: no visible global function definition for 'exonsBy'
computeRPKM: no visible global function definition for 'cdsBy'
computeRPKM: no visible global function definition for
  'intronsByTranscript'
computeRPKM: no visible global function definition for
  'fiveUTRsByTranscript'
computeRPKM: no visible global function definition for
  'threeUTRsByTranscript'
computeRPKM: no visible global function definition for 'seqlevels<-'
computeRPKM: no visible global function definition for 'seqlevels'
computeRPKM: no visible global function definition for 'getBM'
galp2gal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'seqlengths<-'
getAlignGal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'runValue'
getAlignGal: no visible global function definition for 'Rle'
mainSeek: no visible global function definition for 'mclapply'
mainSeekSingleChrom: no visible global function definition for
  'runValue'
mainSeekSingleChrom: no visible global function definition for
  'seqlengths'
plotCoverage: no visible global function definition for 'runValue'
plotCoverage: no visible global function definition for 'seqlengths'
rulebaseRIPSeek: no visible global function definition for 'metadata'
rulebaseRIPSeek: no visible global function definition for 'getBM'
seekRIP: no visible global function definition for 'runValue'
selectBinSize: no visible global function definition for 'seqlengths'
viewRIP: no visible global function definition for 'runValue'
viewRIP: no visible global function definition for
  'GRangesForUCSCGenome'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'SD.aux', 'nar.aux'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [60s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mainSeek              6.22   0.01    6.23
disambiguateMultihits 5.75   0.02    5.77
combineRIP            1.23   0.08   27.98
** running examples for arch 'x64' ... [72s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mainSeek              9.50   0.00    9.50
disambiguateMultihits 8.14   0.00    8.14
combineRIP            1.53   0.03   29.14
* 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: 4 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.


RIPSeeker.Rcheck/00install.out:


install for i386

* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.10.0.zip
* DONE (RIPSeeker)

RIPSeeker.Rcheck/examples_i386/RIPSeeker-Ex.timings:

nameusersystemelapsed
RIPSeeker-package000
addDummyProb0.590.030.63
addPseudoAlignment0.250.000.25
annotateRIP0.020.000.02
binCount0.480.010.50
combineAlignGals0.210.000.20
combineRIP 1.23 0.0827.98
computeLogOdd1.200.001.21
computeRPKM0.020.000.01
disambiguateMultihits5.750.025.77
empiricalFDR000
evalBinSize0.640.000.64
exportGRanges000
galp2gal0.250.000.25
getAlignGal0.110.000.11
logScoreWithControl000
logScoreWithoutControl0.010.000.02
mainSeek6.220.016.23
mainSeekSingleChrom1.050.001.05
nbh.GRanges000
nbh1.720.001.72
nbh.integer000
nbh_chk000
nbh_em0.20.00.2
nbh_gen000
nbh_init1.360.001.36
nbh_vit0.200.000.21
nbm_chk000
nbm_em0.280.000.28
plotCoverage1.020.021.03
plotStrandedCoverage2.000.012.01
randindx0.220.040.25
ripSeek000
rulebaseRIPSeek0.010.000.02
scoreMergedBins000
seekRIP0.020.000.01
selectBinSize2.690.112.80
statdis0.230.000.24
viewRIP000

RIPSeeker.Rcheck/examples_x64/RIPSeeker-Ex.timings:

nameusersystemelapsed
RIPSeeker-package000
addDummyProb0.460.000.47
addPseudoAlignment0.270.000.26
annotateRIP000
binCount1.110.001.11
combineAlignGals0.200.000.21
combineRIP 1.53 0.0329.14
computeLogOdd1.250.011.26
computeRPKM000
disambiguateMultihits8.140.008.14
empiricalFDR000
evalBinSize0.340.000.35
exportGRanges000
galp2gal0.430.000.42
getAlignGal0.120.000.12
logScoreWithControl0.020.000.02
logScoreWithoutControl000
mainSeek9.50.09.5
mainSeekSingleChrom1.290.001.30
nbh.GRanges000
nbh2.830.022.84
nbh.integer000
nbh_chk000
nbh_em0.270.020.28
nbh_gen000
nbh_init1.870.001.88
nbh_vit0.490.000.48
nbm_chk000
nbm_em0.380.000.37
plotCoverage1.310.041.36
plotStrandedCoverage1.970.021.98
randindx0.170.000.18
ripSeek0.020.000.01
rulebaseRIPSeek000
scoreMergedBins0.010.000.02
seekRIP000
selectBinSize3.550.113.65
statdis0.250.000.25
viewRIP000