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CHECK report for QSutils on riesling1

This page was generated on 2020-11-25 12:00:00 -0500 (Wed, 25 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE QSutils PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1380/1907HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QSutils 1.9.0
Mercedes Guerrero-Murillo
Snapshot Date: 2020-11-24 14:41:13 -0500 (Tue, 24 Nov 2020)
URL: https://git.bioconductor.org/packages/QSutils
Branch: master
Last Commit: a1e3237
Last Changed Date: 2020-10-27 11:39:52 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QSutils
Version: 1.9.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QSutils.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings QSutils_1.9.0.tar.gz
StartedAt: 2020-11-24 21:40:58 -0500 (Tue, 24 Nov 2020)
EndedAt: 2020-11-24 21:42:24 -0500 (Tue, 24 Nov 2020)
EllapsedTime: 85.3 seconds
RetCode: 0
Status:  OK  
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QSutils.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings QSutils_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/QSutils.Rcheck'
* using R Under development (unstable) (2020-11-06 r79405)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QSutils/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QSutils' version '1.9.0'
* 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 'QSutils' 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: OK


Installation output

QSutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/QSutils_1.9.0.tar.gz && rm -rf QSutils.buildbin-libdir && mkdir QSutils.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QSutils.buildbin-libdir QSutils_1.9.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL QSutils_1.9.0.zip && rm QSutils_1.9.0.tar.gz QSutils_1.9.0.zip
###
##############################################################################
##############################################################################


  % 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 77247  100 77247    0     0  36.8M      0 --:--:-- --:--:-- --:--:-- 36.8M

install for i386

* installing *source* package 'QSutils' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QSutils'
    finding HTML links ... done
    Collapse                                html  
REDIRECT:topic	 Collapse -> Collapse.html [ SUCCESS ]
REDIRECT:topic	 Recollapse -> Collapse.html [ SUCCESS ]
    ConsSeq                                 html  
REDIRECT:topic	 ConsSeq -> ConsSeq.html [ SUCCESS ]
    CorrectGapsAndNs                        html  
REDIRECT:topic	 CorrectGapsAndNs -> CorrectGapsAndNs.html [ SUCCESS ]
    DBrule                                  html  
REDIRECT:topic	 DBrule -> DBrule.html [ SUCCESS ]
    DNA.dist                                html  
REDIRECT:topic	 DNA.dist -> DNA.dist.html [ SUCCESS ]
    DSFT                                    html  
REDIRECT:topic	 DSFT -> DSFT.html [ SUCCESS ]
    Diverge                                 html  
REDIRECT:topic	 Diverge -> Diverge.html [ SUCCESS ]
    DottedAlignment                         html  
REDIRECT:topic	 DottedAlignment -> DottedAlignment.html [ SUCCESS ]
    FAD                                     html  
REDIRECT:topic	 FAD -> FAD.html [ SUCCESS ]
    FreqMat                                 html  
REDIRECT:topic	 FreqMat -> FreqMat.html [ SUCCESS ]
    GenerateVars                            html  
REDIRECT:topic	 GenerateVars -> GenerateVars.html [ SUCCESS ]
    GenotypeStandards_A-H.fas               html  
REDIRECT:topic	 GenotypeStandards_A-H.fas -> GenotypeStandards_A-H.fas.html [ SUCCESS ]
    GetInfProfile                           html  
REDIRECT:topic	 GetInfProfile -> GetInfProfile.html [ SUCCESS ]
    GetQSData                               html  
REDIRECT:topic	 GetQSData -> GetQSData.html [ SUCCESS ]
    GetRandomSeq                            html  
REDIRECT:topic	 GetRandomSeq -> GetRandomSeq.html [ SUCCESS ]
    GiniSimpson                             html  
REDIRECT:topic	 GiniSimpson -> GiniSimpson.html [ SUCCESS ]
REDIRECT:topic	 GiniSimpsonMVUE -> GiniSimpson.html [ SUCCESS ]
REDIRECT:topic	 GiniSimpsonVar -> GiniSimpson.html [ SUCCESS ]
    HCq                                     html  
REDIRECT:topic	 HCq -> HCq.html [ SUCCESS ]
REDIRECT:topic	 HCqVar -> HCq.html [ SUCCESS ]
REDIRECT:topic	 HCqProfile -> HCq.html [ SUCCESS ]
    Hill                                    html  
REDIRECT:topic	 Hill -> Hill.html [ SUCCESS ]
REDIRECT:topic	 HillProfile -> Hill.html [ SUCCESS ]
    IntersectStrandHpls                     html  
REDIRECT:topic	 IntersectStrandHpls -> IntersectStrandHpls.html [ SUCCESS ]
    MutationFreq                            html  
REDIRECT:topic	 MutationFreq -> MutationFreq.html [ SUCCESS ]
REDIRECT:topic	 MutationFreqVar -> MutationFreq.html [ SUCCESS ]
    MutsTbl                                 html  
REDIRECT:topic	 MutsTbl -> MutsTbl.html [ SUCCESS ]
    NucleotideDiversity                     html  
REDIRECT:topic	 NucleotideDiversity -> NucleotideDiversity.html [ SUCCESS ]
    PolyDist                                html  
REDIRECT:topic	 PolyDist -> PolyDist.html [ SUCCESS ]
    QSutils-package                         html  
REDIRECT:topic	 QSutils-package -> QSutils-package.html [ SUCCESS ]
REDIRECT:topic	 QSutils -> QSutils-package.html [ SUCCESS ]
    Rao                                     html  
REDIRECT:topic	 Rao -> Rao.html [ SUCCESS ]
REDIRECT:topic	 RaoVar -> Rao.html [ SUCCESS ]
REDIRECT:topic	 RaoPow -> Rao.html [ SUCCESS ]
REDIRECT:topic	 RaoPowProfile -> Rao.html [ SUCCESS ]
    ReadAmplSeqs                            html  
REDIRECT:topic	 ReadAmplSeqs -> ReadAmplSeqs.html [ SUCCESS ]
    Renyi                                   html  
REDIRECT:topic	 Renyi -> Renyi.html [ SUCCESS ]
REDIRECT:topic	 RenyiProfile -> Renyi.html [ SUCCESS ]
    ReportVariants                          html  
REDIRECT:topic	 ReportVariants -> ReportVariants.html [ SUCCESS ]
    SegSites                                html  
REDIRECT:topic	 SegSites -> SegSites.html [ SUCCESS ]
    Shannon                                 html  
REDIRECT:topic	 Shannon -> Shannon.html [ SUCCESS ]
REDIRECT:topic	 ShannonVar -> Shannon.html [ SUCCESS ]
REDIRECT:topic	 NormShannon -> Shannon.html [ SUCCESS ]
REDIRECT:topic	 NormShannonVar -> Shannon.html [ SUCCESS ]
    SortByMutations                         html  
REDIRECT:topic	 SortByMutations -> SortByMutations.html [ SUCCESS ]
    SummaryMuts                             html  
REDIRECT:topic	 SummaryMuts -> SummaryMuts.html [ SUCCESS ]
    TotalMutations                          html  
REDIRECT:topic	 TotalMutations -> TotalMutations.html [ SUCCESS ]
    Toy.GapsAndNs.fna                       html  
REDIRECT:topic	 Toy.GapsAndNs.fna -> Toy.GapsAndNs.fna.html [ SUCCESS ]
    ToyData_10_50_1000.fna                  html  
REDIRECT:topic	 ToyData_10_50_1000.fna -> ToyData_10_50_1000.fna.html [ SUCCESS ]
    ToyData_FWReads.fna                     html  
REDIRECT:topic	 ToyData_FWReads.fna -> ToyData_FWReads.fna.html [ SUCCESS ]
    ToyData_RVReads.fna                     html  
REDIRECT:topic	 ToyData_RVReads.fna -> ToyData_RVReads.fna.html [ SUCCESS ]
    UniqueMutations                         html  
REDIRECT:topic	 UniqueMutations -> UniqueMutations.html [ SUCCESS ]
    Unknown-Genotype.fna                    html  
REDIRECT:topic	 Unknown-Genotype.fna -> Unknown-Genotype.fna.html [ SUCCESS ]
    fn.ab                                   html  
REDIRECT:topic	 fn.ab -> fn.ab.html [ SUCCESS ]
    geom.series                             html  
REDIRECT:topic	 geom.series -> geom.series.html [ SUCCESS ]
** 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 'QSutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QSutils' as QSutils_1.9.0.zip
* DONE (QSutils)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'QSutils' successfully unpacked and MD5 sums checked

Tests output


Example timings

QSutils.Rcheck/examples_i386/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.070.020.08
ConsSeq0.010.000.02
CorrectGapsAndNs0.010.000.02
DBrule0.030.000.03
DNA.dist000
DSFT000
Diverge000
DottedAlignment000
FAD0.020.000.01
FreqMat0.030.000.03
GenerateVars000
GenotypeStandards_A-H.fas000
GetInfProfile0.010.000.02
GetQSData0.330.030.36
GetRandomSeq000
GiniSimpson000
HCq000
Hill0.020.000.02
IntersectStrandHpls0.070.000.08
MutationFreq0.350.020.36
MutsTbl0.030.000.03
NucleotideDiversity000
PolyDist0.010.000.02
Rao0.020.000.02
ReadAmplSeqs0.030.000.03
Renyi0.020.000.01
ReportVariants0.010.000.02
SegSites000
Shannon000
SortByMutations0.340.040.39
SummaryMuts000
TotalMutations000
Toy.GapsAndNs.fna0.030.000.03
ToyData_10_50_1000.fna0.020.000.01
ToyData_FWReads.fna0.050.000.05
ToyData_RVReads.fna0.030.000.03
UniqueMutations000
Unknown-Genotype.fna0.000.020.02
fn.ab000
geom.series000

QSutils.Rcheck/examples_x64/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.080.010.10
ConsSeq0.010.000.01
CorrectGapsAndNs000
DBrule0.000.030.03
DNA.dist0.000.020.02
DSFT0.020.000.02
Diverge000
DottedAlignment000
FAD000
FreqMat0.010.000.02
GenerateVars000
GenotypeStandards_A-H.fas000
GetInfProfile0.020.000.02
GetQSData0.470.020.49
GetRandomSeq000
GiniSimpson000
HCq000
Hill0.020.000.02
IntersectStrandHpls0.040.000.05
MutationFreq0.410.000.40
MutsTbl0.020.000.02
NucleotideDiversity0.010.000.01
PolyDist0.020.000.02
Rao000
ReadAmplSeqs0.010.000.02
Renyi000
ReportVariants0.020.000.01
SegSites0.010.000.02
Shannon000
SortByMutations0.530.010.54
SummaryMuts0.020.000.02
TotalMutations0.020.000.02
Toy.GapsAndNs.fna0.040.000.05
ToyData_10_50_1000.fna0.020.000.02
ToyData_FWReads.fna0.060.000.07
ToyData_RVReads.fna0.060.000.06
UniqueMutations0.020.000.01
Unknown-Genotype.fna0.010.000.02
fn.ab000
geom.series000