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

This page was generated on 2015-10-27 17:31:30 -0400 (Tue, 27 Oct 2015).

Package 496/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiReadsProcessor 1.6.0
Nirav V Malani
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/hiReadsProcessor
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: hiReadsProcessor
Version: 1.6.0
Command: rm -rf hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && mkdir hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiReadsProcessor.buildbin-libdir hiReadsProcessor_1.6.0.tar.gz >hiReadsProcessor.Rcheck\00install.out 2>&1 && cp hiReadsProcessor.Rcheck\00install.out hiReadsProcessor-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=hiReadsProcessor.buildbin-libdir --install="check:hiReadsProcessor-install.out" --force-multiarch --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz
StartedAt: 2015-10-27 02:44:08 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:49:27 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 319.4 seconds
RetCode: 0
Status:  OK  
CheckDir: hiReadsProcessor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && mkdir hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiReadsProcessor.buildbin-libdir hiReadsProcessor_1.6.0.tar.gz >hiReadsProcessor.Rcheck\00install.out 2>&1 && cp hiReadsProcessor.Rcheck\00install.out hiReadsProcessor-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=hiReadsProcessor.buildbin-libdir --install="check:hiReadsProcessor-install.out" --force-multiarch --no-vignettes --timings hiReadsProcessor_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/hiReadsProcessor.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 'hiReadsProcessor/DESCRIPTION' ... OK
* this is package 'hiReadsProcessor' version '1.6.0'
* 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 whether package 'hiReadsProcessor' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chunkize: no visible global function definition for 'breakInChunks'
chunkize: no visible global function definition for 'detectCores'
clusterSites: no visible binding for global variable 'n'
clusterSites: no visible global function definition for 'desc'
clusterSites: no visible global function definition for 'contains'
clusterSites: no visible binding for global variable 'clusteredValue'
clusterSites: no visible binding for global variable
  'clusteredValue.freq'
crossOverCheck: no visible binding for global variable 'n'
decodeByBarcode: no visible global function definition for 'metadata<-'
decodeByBarcode: no visible global function definition for 'metadata'
extractSeqs : <anonymous>: no visible global function definition for
  'metadata'
extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'IRanges'
extractSeqs : <anonymous> : <anonymous>: no visible global function
  definition for 'IRanges'
findBarcodes: no visible global function definition for 'metadata<-'
findBarcodes: no visible global function definition for 'metadata'
findIntegrations : <anonymous>: no visible global function definition
  for 'IRanges'
findVector : <anonymous>: no visible global function definition for
  'IRanges'
getSonicAbund: no visible binding for global variable 'n'
pairwiseAlignSeqs: no visible global function definition for
  'IRangesList'
pairwiseAlignSeqs: no visible global function definition for 'IRanges'
primerIDAlignSeqs: no visible global function definition for 'IRanges'
primerIDAlignSeqs: no visible global function definition for
  'IRangesList'
pslToRangedObject: no visible global function definition for 'IRanges'
read.BAMasPSL: no visible global function definition for 'ScanBamParam'
read.BAMasPSL: no visible global function definition for 'scanBamFlag'
read.BAMasPSL: no visible global function definition for 'DataFrame'
read.SeqFolder: no visible global function definition for 'SimpleList'
read.psl: no visible global function definition for 'mclapply'
read.psl : <anonymous>: no visible binding for global variable
  'matches'
read.psl : <anonymous>: no visible binding for global variable
  'misMatches'
read.psl : <anonymous>: no visible binding for global variable
  'qBaseInsert'
read.psl : <anonymous>: no visible binding for global variable
  'tBaseInsert'
read.psl: no visible binding for global variable 'matches'
read.psl: no visible binding for global variable 'misMatches'
read.psl: no visible binding for global variable 'qBaseInsert'
read.psl: no visible binding for global variable 'tBaseInsert'
read.sampleInfo: no visible global function definition for 'SimpleList'
troubleshootLinkers : <anonymous>: no visible global function
  definition for 'try_default'
vpairwiseAlignSeqs: no visible global function definition for 'Rle'
vpairwiseAlignSeqs: no visible global function definition for
  'runLength'
vpairwiseAlignSeqs: no visible global function definition for 'IRanges'
vpairwiseAlignSeqs: no visible global function definition for
  'runValue'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
** running examples for arch 'x64' ... [27s] 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 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/hiReadsProcessor.Rcheck/00check.log'
for details.


hiReadsProcessor.Rcheck/00install.out:


install for i386

* installing *source* package 'hiReadsProcessor' ...
** R
** data
** 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 'hiReadsProcessor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiReadsProcessor' as hiReadsProcessor_1.6.0.zip
* DONE (hiReadsProcessor)

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

nameusersystemelapsed
addFeature0.110.000.11
addListNameToReads0.30.00.3
annotateSites000
blatSeqs000
chunkize0.030.000.03
clusterSites000
crossOverCheck0.090.000.09
dereplicateReads0.030.000.03
doRCtest0.030.000.03
extractFeature0.110.000.11
extractSeqs0.530.010.55
findAndTrimSeq0.830.050.88
findBarcodes0.350.000.34
findIntegrations000
findLTRs000
findLinkers000
findPrimers000
findVector000
getIntegrationSites0.720.000.72
getSectorsForSamples0.170.000.18
getSonicAbund1.160.041.20
isuSites1.170.021.19
otuSites1.270.001.26
pairUpAlignments000
pairwiseAlignSeqs1.600.031.64
primerIDAlignSeqs1.610.061.67
pslCols000
pslToRangedObject0.070.000.07
read.BAMasPSL000
read.SeqFolder1.970.022.22
read.blast8000
read.psl000
read.sampleInfo2.060.002.06
read.seqsFromSector000
removeReadsWithNs0.030.000.03
replicateReads0.050.000.05
sampleSummary0.700.030.73
splitByBarcode0.030.000.03
splitSeqsToFiles000
startgfServer000
trimSeqs0.030.000.03
vpairwiseAlignSeqs0.610.000.61
write.listedDNAStringSet000
write.psl0.030.020.05

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

nameusersystemelapsed
addFeature0.090.000.10
addListNameToReads0.360.000.36
annotateSites000
blatSeqs000
chunkize0.050.000.04
clusterSites000
crossOverCheck0.100.000.11
dereplicateReads0.360.000.36
doRCtest0.040.000.03
extractFeature0.090.010.11
extractSeqs0.610.000.61
findAndTrimSeq1.250.001.25
findBarcodes0.370.000.38
findIntegrations000
findLTRs000
findLinkers000
findPrimers000
findVector000
getIntegrationSites0.750.000.75
getSectorsForSamples0.100.000.09
getSonicAbund0.760.050.81
isuSites1.670.001.68
otuSites1.800.001.79
pairUpAlignments000
pairwiseAlignSeqs1.440.051.49
primerIDAlignSeqs1.640.011.65
pslCols000
pslToRangedObject0.070.000.08
read.BAMasPSL000
read.SeqFolder2.000.021.90
read.blast8000
read.psl000
read.sampleInfo2.550.002.53
read.seqsFromSector000
removeReadsWithNs0.030.000.04
replicateReads0.060.000.06
sampleSummary0.630.000.62
splitByBarcode0.030.000.03
splitSeqsToFiles000
startgfServer000
trimSeqs0.030.000.04
vpairwiseAlignSeqs0.740.000.73
write.listedDNAStringSet000
write.psl0.030.000.03