Multiple platform build/check report for BioC 3.9 - CHECK report for sigaR on tokay2

Package: sigaR

Version: 1.31.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigaR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sigaR_1.31.0.tar.gz

StartedAt: 2019-04-09 05:56:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:02:03 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 348.9 seconds

RetCode: 0

Status: OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigaR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sigaR_1.31.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/sigaR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.31.0'
* 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 'sigaR' 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.alphabivariate' '.alphaest' '.pretest'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mutInfTest    86.53   2.75   89.34
cisEffectTune 12.55   0.00   12.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mutInfTest    91.52   1.64   93.15
cisEffectTune 10.52   0.00   10.52
* 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:/Users/biocbuild/bbs-3.9-bioc/meat/sigaR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/sigaR_1.31.0.tar.gz && rm -rf sigaR.buildbin-libdir && mkdir sigaR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigaR.buildbin-libdir sigaR_1.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL sigaR_1.31.0.zip && rm sigaR_1.31.0.tar.gz sigaR_1.31.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  119k  100  119k    0     0  1979k      0 --:--:-- --:--:-- --:--:-- 2250k

install for i386

* installing *source* package 'sigaR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sigaR'
    finding HTML links ... done
    CNGEheatmaps                            html  
    ExpressionSet2order                     html  
    finding level-2 HTML links ... done

    ExpressionSet2subset                    html  
    ExpressionSet2weightedSubset            html  
    RCMestimation                           html  
    RCMrandom-method                        html  
    RCMrandom                               html  
    RCMtest                                 html  
    cghCall2cghSeg                          html  
    cghCall2maximumSubset                   html  
    cghCall2order                           html  
    cghCall2subset                          html  
    cghCall2weightedSubset                  html  
    cghSeg2order                            html  
    cghSeg2subset                           html  
    cghSeg2weightedSubset                   html  
    cisEffectPlot                           html  
    cisEffectTable                          html  
    cisEffectTest                           html  
    cisEffectTune                           html  
    cisTest-class                           html  
    entTest-class                           html  
    entropyTest                             html  
    expandMatching2singleIDs                html  
    getSegFeatures                          html  
    hdEntropy                               html  
    hdMI                                    html  
    matchAnn2Ann                            html  
    matchCGHcall2ExpressionSet              html  
    merge2ExpressionSets                    html  
    merge2cghCalls                          html  
    miTest-class                            html  
    mutInfTest                              html  
    nBreakpoints                            html  
    pathway1sample                          html  
    pathway2sample                          html  
    pathwayFit-class                        html  
    pathwayPlot                             html  
    pollackCN16                             html  
    pollackGE16                             html  
    profilesPlot                            html  
    rcmFit-class                            html  
    rcmTest-class                           html  
    sigaR-package                           html  
    splitMatchingAtBreakpoints              html  
    summary-method                          html  
    uniqGenomicInfo                         html  
    z.RCMloss-method                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'sigaR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigaR' as sigaR_1.31.0.zip
* DONE (sigaR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'sigaR' successfully unpacked and MD5 sums checked

name	user	system	elapsed
CNGEheatmaps	1.08	0.10	1.17
ExpressionSet2order	0.02	0.01	0.03
ExpressionSet2subset	0.02	0.00	0.02
ExpressionSet2weightedSubset	0.29	0.02	0.29
RCMestimation	0.61	0.06	0.67
RCMrandom	0.59	0.00	0.59
RCMtest	3.44	0.03	3.47
cghCall2cghSeg	0.1	0.0	0.1
cghCall2maximumSubset	0.48	0.02	0.50
cghCall2order	0.02	0.00	0.01
cghCall2subset	0.04	0.00	0.05
cghCall2weightedSubset	0.38	0.00	0.37
cghSeg2order	0.04	0.00	0.05
cghSeg2subset	0.08	0.00	0.07
cghSeg2weightedSubset	0.42	0.00	0.43
cisEffectPlot	0.08	0.02	0.09
cisEffectTable	1.60	0.04	1.64
cisEffectTest	1.82	0.04	1.86
cisEffectTune	12.55	0.00	12.54
cisTest-class	0	0	0
entTest-class	0	0	0
entropyTest	0.34	0.00	0.35
expandMatching2singleIDs	0.01	0.01	0.03
getSegFeatures	0.00	0.02	0.02
hdEntropy	0.02	0.00	0.02
hdMI	0.72	0.02	0.73
matchAnn2Ann	0.01	0.00	0.02
matchCGHcall2ExpressionSet	0.03	0.01	0.05
merge2ExpressionSets	0.05	0.00	0.04
merge2cghCalls	0.05	0.00	0.05
miTest-class	0	0	0
mutInfTest	86.53	2.75	89.34
nBreakpoints	0.17	0.03	0.21
pathway1sample	0.13	0.00	0.12
pathway2sample	2.87	0.54	3.41
pathwayFit-class	0	0	0
pathwayPlot	0.06	0.00	0.06
pollackCN16	0	0	0
pollackGE16	0.00	0.01	0.01
profilesPlot	0.08	0.02	0.10
rcmFit-class	0	0	0
rcmTest-class	0	0	0
splitMatchingAtBreakpoints	0.12	0.00	0.12
uniqGenomicInfo	0.02	0.00	0.02

name	user	system	elapsed
CNGEheatmaps	0.90	0.03	0.94
ExpressionSet2order	0.00	0.02	0.01
ExpressionSet2subset	0.01	0.00	0.01
ExpressionSet2weightedSubset	0.3	0.0	0.3
RCMestimation	0.73	0.02	0.75
RCMrandom	0.94	0.01	0.95
RCMtest	3.27	0.00	3.26
cghCall2cghSeg	0.09	0.00	0.10
cghCall2maximumSubset	0.49	0.00	0.48
cghCall2order	0.01	0.01	0.03
cghCall2subset	0.05	0.00	0.05
cghCall2weightedSubset	0.36	0.02	0.37
cghSeg2order	0.04	0.00	0.05
cghSeg2subset	0.07	0.00	0.06
cghSeg2weightedSubset	0.28	0.00	0.29
cisEffectPlot	0.04	0.01	0.06
cisEffectTable	1.29	0.02	1.29
cisEffectTest	1.26	0.00	1.27
cisEffectTune	10.52	0.00	10.52
cisTest-class	0	0	0
entTest-class	0	0	0
entropyTest	0.29	0.00	0.29
expandMatching2singleIDs	0.02	0.01	0.03
getSegFeatures	0.02	0.00	0.02
hdEntropy	0.01	0.00	0.02
hdMI	0.70	0.02	0.71
matchAnn2Ann	0.02	0.02	0.04
matchCGHcall2ExpressionSet	0.03	0.01	0.04
merge2ExpressionSets	0.05	0.00	0.05
merge2cghCalls	0.04	0.00	0.05
miTest-class	0	0	0
mutInfTest	91.52	1.64	93.15
nBreakpoints	0.23	0.02	0.25
pathway1sample	0.13	0.00	0.13
pathway2sample	2.66	0.64	3.29
pathwayFit-class	0	0	0
pathwayPlot	0.09	0.00	0.10
pollackCN16	0.00	0.01	0.01
pollackGE16	0.02	0.00	0.02
profilesPlot	0.09	0.00	0.09
rcmFit-class	0	0	0
rcmTest-class	0	0	0
splitMatchingAtBreakpoints	0.16	0.00	0.16
uniqGenomicInfo	0.00	0.02	0.01

CHECK report for sigaR on tokay2

Summary

Command output

Installation output

Tests output

Example timings