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CHECK report for QSutils on tokay1

This page was generated on 2019-04-13 11:29:50 -0400 (Sat, 13 Apr 2019).

Package 1228/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QSutils 1.0.0
Mercedes Guerrero-Murillo
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/QSutils
Branch: RELEASE_3_8
Last Commit: 85827df
Last Changed Date: 2018-10-30 11:42:11 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QSutils
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QSutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings QSutils_1.0.0.tar.gz
StartedAt: 2019-04-13 04:47:05 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:49:33 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 147.9 seconds
RetCode: 0
Status:  OK  
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QSutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings QSutils_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/QSutils.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/QSutils_1.0.0.tar.gz && rm -rf QSutils.buildbin-libdir && mkdir QSutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QSutils.buildbin-libdir QSutils_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL QSutils_1.0.0.zip && rm QSutils_1.0.0.tar.gz QSutils_1.0.0.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 74620  100 74620    0     0  1826k      0 --:--:-- --:--:-- --:--:-- 2024k

install for i386

* installing *source* package 'QSutils' ...
** 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  
    ConsSeq                                 html  
    CorrectGapsAndNs                        html  
    DBrule                                  html  
    DNA.dist                                html  
    DSFT                                    html  
    Diverge                                 html  
    DottedAlignment                         html  
    FAD                                     html  
    FreqMat                                 html  
    GenerateVars                            html  
    GenotypeStandards_A-H.fas               html  
    GetInfProfile                           html  
    GetQSData                               html  
    GetRandomSeq                            html  
    GiniSimpson                             html  
    HCq                                     html  
    Hill                                    html  
    IntersectStrandHpls                     html  
    MutationFreq                            html  
    MutsTbl                                 html  
    NucleotideDiversity                     html  
    PolyDist                                html  
    QSutils-package                         html  
    Rao                                     html  
    ReadAmplSeqs                            html  
    Renyi                                   html  
    ReportVariants                          html  
    SegSites                                html  
    Shannon                                 html  
    SortByMutations                         html  
    SummaryMuts                             html  
    TotalMutations                          html  
    Toy.GapsAndNs.fna                       html  
    ToyData_10_50_1000.fna                  html  
    ToyData_FWReads.fna                     html  
    ToyData_RVReads.fna                     html  
    UniqueMutations                         html  
    Unknown-Genotype.fna                    html  
    fn.ab                                   html  
    geom.series                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'QSutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QSutils' as QSutils_1.0.0.zip
* DONE (QSutils)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'QSutils' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

QSutils.Rcheck/examples_i386/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.320.000.44
ConsSeq0.020.000.03
CorrectGapsAndNs000
DBrule0.040.000.06
DNA.dist000
DSFT0.010.000.02
Diverge000
DottedAlignment0.020.000.01
FAD000
FreqMat0.010.000.02
GenerateVars000
GenotypeStandards_A-H.fas0.020.000.01
GetInfProfile0.000.030.03
GetQSData0.400.000.41
GetRandomSeq000
GiniSimpson000
HCq0.020.000.02
Hill000
IntersectStrandHpls0.050.000.40
MutationFreq0.270.020.28
MutsTbl0.010.000.01
NucleotideDiversity0.000.010.02
PolyDist0.020.000.02
Rao0.000.020.01
ReadAmplSeqs0.030.000.03
Renyi000
ReportVariants0.020.000.02
SegSites0.000.010.01
Shannon000
SortByMutations0.360.000.36
SummaryMuts0.010.000.02
TotalMutations0.020.000.01
Toy.GapsAndNs.fna0.040.000.05
ToyData_10_50_1000.fna0.040.000.03
ToyData_FWReads.fna0.060.000.06
ToyData_RVReads.fna0.060.000.07
UniqueMutations000
Unknown-Genotype.fna0.020.000.01
fn.ab000
geom.series000

QSutils.Rcheck/examples_x64/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.190.000.19
ConsSeq0.030.000.03
CorrectGapsAndNs0.010.000.01
DBrule0.280.000.29
DNA.dist0.020.000.01
DSFT000
Diverge000
DottedAlignment0.020.000.02
FAD000
FreqMat0.010.000.01
GenerateVars0.020.000.02
GenotypeStandards_A-H.fas000
GetInfProfile0.010.000.01
GetQSData0.390.020.41
GetRandomSeq000
GiniSimpson000
HCq000
Hill0.020.000.02
IntersectStrandHpls0.080.000.07
MutationFreq0.500.010.52
MutsTbl0.010.000.02
NucleotideDiversity000
PolyDist0.030.000.03
Rao0.020.000.01
ReadAmplSeqs0.010.000.02
Renyi0.020.000.01
ReportVariants0.020.000.02
SegSites000
Shannon000
SortByMutations0.510.020.53
SummaryMuts0.020.000.02
TotalMutations0.030.000.03
Toy.GapsAndNs.fna0.050.000.04
ToyData_10_50_1000.fna0.010.000.02
ToyData_FWReads.fna0.050.010.06
ToyData_RVReads.fna0.060.000.06
UniqueMutations0.020.000.02
Unknown-Genotype.fna0.010.000.02
fn.ab000
geom.series000