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BioC 3.3: CHECK report for AllelicImbalance on moscato2

This page was generated on 2016-10-13 12:51:55 -0700 (Thu, 13 Oct 2016).

Package 36/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AllelicImbalance 1.10.2
Jesper R Gadin
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AllelicImbalance
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  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: AllelicImbalance
Version: 1.10.2
Command: rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.10.2.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.10.2.tar.gz
StartedAt: 2016-10-13 00:52:05 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:11:02 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1137.8 seconds
RetCode: 0
Status:  OK  
CheckDir: AllelicImbalance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && mkdir AllelicImbalance.buildbin-libdir AllelicImbalance.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AllelicImbalance.buildbin-libdir AllelicImbalance_1.10.2.tar.gz >AllelicImbalance.Rcheck\00install.out 2>&1 && cp AllelicImbalance.Rcheck\00install.out AllelicImbalance-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AllelicImbalance.buildbin-libdir --install="check:AllelicImbalance-install.out" --force-multiarch --no-vignettes --timings AllelicImbalance_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AllelicImbalance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AllelicImbalance' version '1.10.2'
* package encoding: UTF-8
* 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 'AllelicImbalance' 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
.array2MatrixList: no visible global function definition for 'setNames'
.lvaRegressionPvalue : <anonymous>: no visible global function
  definition for 'lm'
.lvaRegressionReturnCommonParamMatrix : <anonymous>: no visible global
  function definition for 'lm'
.lvaRegressionReturnCommonParamMatrixTxSNPspecific: no visible global
  function definition for 'lm'
decorateWithExons: no visible global function definition for 'lines'
decorateWithExons: no visible global function definition for 'text'
decorateWithGenes: no visible global function definition for 'lines'
decorateWithGenes: no visible global function definition for 'text'
legendBarplot: no visible global function definition for 'symbols'
legendBarplot: no visible global function definition for 'text'
barplot,ASEset: no visible global function definition for
  'plot.default'
barplot,ASEset: no visible global function definition for 'symbols'
barplot,ASEset: no visible global function definition for 'lines'
barplot,ASEset : <anonymous>: no visible global function definition for
  'lines'
barplot,ASEset: no visible global function definition for 'text'
barplot,ASEset: no visible global function definition for 'title'
barplot,ASEset: no visible global function definition for 'dist'
locationplot,ASEset: no visible global function definition for
  'plot.default'
locationplot,ASEset: no visible global function definition for 'lines'
locationplot,ASEset: no visible global function definition for 'points'
locationplot,ASEset: no visible global function definition for 'abline'
plot,LinkVariantAlmlof-ANY: no visible global function definition for
  'abline'
plot,LinkVariantAlmlof-ANY: no visible global function definition for
  'mtext'
reference_frequency_density_vs_threshold_variable_plot,DetectedAI: no
  visible global function definition for 'heat.colors'
Undefined global functions or variables:
  abline dist heat.colors lines lm mtext plot.default points setNames
  symbols text title
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "lines", "mtext", "plot.default",
             "points", "symbols", "text", "title")
  importFrom("stats", "dist", "lm", "setNames")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     82.54   1.81  115.70
import-bam               11.64   0.03   11.67
annotation-wrappers       7.66   0.33  258.43
getAlleleQuality          6.23   0.01    6.24
scanForHeterozygotes-old  6.10   0.00    6.10
getAlleleCounts           5.38   0.02    5.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getSnpIdFromLocation     83.01   1.62   85.24
import-bam               19.12   0.05   19.23
annotation-wrappers       8.02   0.23    8.77
scanForHeterozygotes-old  7.94   0.00    7.94
getAlleleCounts           7.62   0.03    7.72
getAlleleQuality          7.03   0.00    7.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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 NOTE
See
  'E:/biocbld/bbs-3.3-bioc/meat/AllelicImbalance.Rcheck/00check.log'
for details.


AllelicImbalance.Rcheck/00install.out:


install for i386

* installing *source* package 'AllelicImbalance' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'hist' from package 'graphics' in package 'AllelicImbalance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AllelicImbalance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AllelicImbalance' as AllelicImbalance_1.10.2.zip
* DONE (AllelicImbalance)

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

nameusersystemelapsed
ASEset-barplot0.220.000.22
ASEset-class0.800.000.79
ASEset-filters0.060.000.06
ASEset-gbarplot0.030.020.05
ASEset-glocationplot1.690.011.70
ASEset-gviztrack0.390.000.39
ASEset-scanForHeterozygotes2.960.022.98
ASEset.old000
ASEset.sim000
ASEsetFromBam0.000.010.02
DetectedAI-class0.060.000.06
DetectedAI-plot1.280.001.29
DetectedAI-summary0.070.030.10
GRvariants000
GlobalAnalysis-class0.000.020.01
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.010.001.02
RegionSummary-class000
RiskVariant-class000
annotation-wrappers 7.66 0.33258.43
annotationBarplot000
barplot-lattice-support0.160.000.16
binom.test0.030.000.03
chisq.test0.050.000.05
cigar-utilities0.010.000.01
countAllelesFromBam000
coverageMatrixListFromGAL1.160.001.16
decorateWithExons000
decorateWithGenes000
defaultMapBias0.030.000.03
defaultPhase000
detectAI0.060.000.06
fractionPlotDf0.020.010.03
gba000
genomatrix000
genotype2phase0.020.000.02
getAlleleCounts5.380.025.63
getAlleleQuality6.230.016.24
getAreaFromGeneNames0.390.020.40
getDefaultMapBiasExpMean0.010.000.02
getSnpIdFromLocation 82.54 1.81115.70
histplot000
implodeList-old000
import-bam-2000
import-bam11.64 0.0311.67
import-bcf0.640.000.64
inferAlleles0.010.020.03
inferAltAllele0.030.000.03
inferGenotypes0.050.000.05
initialize-ASEset0.050.000.04
initialize-DetectedAI0.070.010.10
initialize-GlobalAnalysis0.000.020.01
initialize-RiskVariant0.000.010.02
legendBarplot000
locationplot0.570.000.56
lva1.910.001.92
lva.internal0.210.000.31
makeMaskedFasta0.610.000.73
mapBiasRef0.020.000.02
minCountFilt0.030.000.03
minFreqFilt0.030.020.04
multiAllelicFilt0.010.000.02
phase2genotype0.020.010.03
phaseArray2phaseMatrix0.020.000.02
phaseMatrix2Array000
randomRef0.020.000.02
reads000
refAllele0.010.000.01
regionSummary0.390.020.41
scanForHeterozygotes-old6.10.06.1

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

nameusersystemelapsed
ASEset-barplot0.640.001.47
ASEset-class0.340.000.34
ASEset-filters0.050.000.05
ASEset-gbarplot0.030.000.03
ASEset-glocationplot2.370.003.57
ASEset-gviztrack1.160.001.15
ASEset-scanForHeterozygotes3.610.014.08
ASEset.old000
ASEset.sim000
ASEsetFromBam000
DetectedAI-class0.130.000.17
DetectedAI-plot1.790.021.81
DetectedAI-summary0.100.000.09
GRvariants0.010.000.02
GlobalAnalysis-class000
LinkVariantAlmlof-class000
LinkVariantAlmlof-plot1.250.001.24
RegionSummary-class000
RiskVariant-class000
annotation-wrappers8.020.238.77
annotationBarplot000
barplot-lattice-support0.180.000.17
binom.test0.040.000.05
chisq.test0.050.000.04
cigar-utilities0.020.000.02
countAllelesFromBam0.000.020.01
coverageMatrixListFromGAL1.020.001.03
decorateWithExons000
decorateWithGenes0.020.000.02
defaultMapBias0.050.010.37
defaultPhase000
detectAI0.110.000.11
fractionPlotDf0.060.000.06
gba000
genomatrix000
genotype2phase0.000.020.02
getAlleleCounts7.620.037.72
getAlleleQuality7.030.007.03
getAreaFromGeneNames0.470.030.50
getDefaultMapBiasExpMean0.020.000.02
getSnpIdFromLocation83.01 1.6285.24
histplot000
implodeList-old000
import-bam-2000
import-bam19.12 0.0519.23
import-bcf0.920.000.94
inferAlleles0.020.000.01
inferAltAllele0.030.000.04
inferGenotypes0.050.000.04
initialize-ASEset0.060.000.07
initialize-DetectedAI0.110.000.10
initialize-GlobalAnalysis0.010.000.01
initialize-RiskVariant0.000.020.02
legendBarplot000
locationplot0.600.010.61
lva2.020.002.02
lva.internal0.250.000.25
makeMaskedFasta1.020.021.06
mapBiasRef0.020.000.02
minCountFilt0.060.010.07
minFreqFilt0.060.000.07
multiAllelicFilt0.020.020.03
phase2genotype0.030.000.03
phaseArray2phaseMatrix0.010.000.02
phaseMatrix2Array0.020.000.02
randomRef0.010.010.03
reads000
refAllele0.020.020.03
regionSummary0.680.020.70
scanForHeterozygotes-old7.940.007.94