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CHECK report for qsea on tokay1

This page was generated on 2019-04-13 11:26:51 -0400 (Sat, 13 Apr 2019).

Package 1227/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.8.0
Matthias Lienhard
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/qsea
Branch: RELEASE_3_8
Last Commit: 7e31008
Last Changed Date: 2018-10-30 11:42:01 -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: qsea
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings qsea_1.8.0.tar.gz
StartedAt: 2019-04-13 04:46:59 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:56:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 576.0 seconds
RetCode: 0
Status:  OK  
CheckDir: qsea.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:qsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings qsea_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/qsea.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 'qsea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qsea' version '1.8.0'
* 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 'qsea' 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/qsea/libs/i386/qsea.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
addNewSamples     92.12   2.86  103.77
addCNV            13.94   1.18   20.72
addCoverage       12.00   0.04   12.03
addPatternDensity  7.81   0.20    8.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
addNewSamples     78.53   0.77   79.30
addCNV            14.81   0.31   15.12
addCoverage        8.70   0.05    8.75
addPatternDensity  7.81   0.17    7.98
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/qsea.Rcheck/00check.log'
for details.



Installation output

qsea.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/qsea_1.8.0.tar.gz && rm -rf qsea.buildbin-libdir && mkdir qsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qsea.buildbin-libdir qsea_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL qsea_1.8.0.zip && rm qsea_1.8.0.tar.gz qsea_1.8.0.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  285k  100  285k    0     0  3191k      0 --:--:-- --:--:-- --:--:-- 3318k

install for i386

* installing *source* package 'qsea' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c lm.c -o lm.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/qsea.buildbin-libdir/qsea/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'qsea'
    finding HTML links ... done
    addCNV                                  html  
    addContrast                             html  
    addCoverage                             html  
    addEnrichmentParameters                 html  
    addLibraryFactors                       html  
    addNewSamples                           html  
    addOffset                               html  
    addPatternDensity                       html  
    addSeqPref                              html  
    createQseaSet                           html  
    example                                 html  
    fitNBglm                                html  
    getPCA                                  html  
    isSignificant                           html  
    makeTable                               html  
    normMethod                              html  
    plotCNV                                 html  
    plotCoverage                            html  
    plotEnrichmentProfile                   html  
    plotPCA                                 html  
    qsea-package                            html  
    qseaGLM-class                           html  
    qseaPCA-class                           html  
    qseaSet-class                           html  
    regionStats                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'qsea' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lm.c -o lm.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/qsea.buildbin-libdir/qsea/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qsea' as qsea_1.8.0.zip
* DONE (qsea)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'qsea' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

qsea.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(qsea)
> 
> test_check("qsea")
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.53    0.71    9.23 

qsea.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(qsea)
> 
> test_check("qsea")
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.73    0.29   10.01 

Example timings

qsea.Rcheck/examples_i386/qsea-Ex.timings

nameusersystemelapsed
addCNV13.94 1.1820.72
addContrast1.360.281.64
addCoverage12.00 0.0412.03
addEnrichmentParameters0.390.070.47
addLibraryFactors1.280.221.50
addNewSamples 92.12 2.86103.77
addOffset0.280.020.29
addPatternDensity7.810.208.02
createQseaSet0.140.020.15
example0.170.000.17
fitNBglm1.220.031.25
getPCA0.610.000.61
isSignificant0.980.000.99
makeTable1.180.001.17
normMethod000
plotCNV0.20.00.2
plotCoverage0.550.000.55
plotEnrichmentProfile0.280.000.28
plotPCA0.530.010.55
qseaGLM-class000
qseaPCA-class000
qseaSet-class000
regionStats0.450.000.45

qsea.Rcheck/examples_x64/qsea-Ex.timings

nameusersystemelapsed
addCNV14.81 0.3115.12
addContrast2.890.002.89
addCoverage8.700.058.75
addEnrichmentParameters0.350.000.35
addLibraryFactors1.200.031.23
addNewSamples78.53 0.7779.30
addOffset0.280.000.28
addPatternDensity7.810.177.98
createQseaSet0.240.010.25
example0.260.000.27
fitNBglm1.690.021.71
getPCA0.610.000.61
isSignificant1.060.001.06
makeTable1.330.021.34
normMethod000
plotCNV0.220.000.22
plotCoverage0.590.000.60
plotEnrichmentProfile0.280.010.29
plotPCA0.50.00.5
qseaGLM-class000
qseaPCA-class000
qseaSet-class000
regionStats0.520.000.52