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CHECK report for IntEREst on tokay1

This page was generated on 2021-05-05 12:12:13 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the IntEREst package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 904/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.14.0  (landing page)
Ali Oghabian , Mikko Frilander
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/IntEREst
Branch: RELEASE_3_12
Last Commit: 514e896
Last Changed Date: 2020-10-27 11:22:16 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: IntEREst
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IntEREst.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IntEREst_1.14.0.tar.gz
StartedAt: 2021-05-05 03:53:27 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 04:02:57 -0400 (Wed, 05 May 2021)
EllapsedTime: 569.8 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: IntEREst.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IntEREst.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IntEREst_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/IntEREst.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IntEREst/DESCRIPTION' ... OK
* this is package 'IntEREst' version '1.14.0'
* 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 'IntEREst' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp23NHlq/R.INSTALL25cc3e7248d4/IntEREst/man/u12DensityPlot.Rd:123: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/IntEREst.Rcheck/00install.out' for details.
* 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 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 (user + system) or elapsed time > 5s
                user system elapsed
DEXSeqIntEREst 22.87   0.72   23.68
deseqInterest   6.13   0.14    6.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
DEXSeqIntEREst 35.20   0.16   35.36
deseqInterest   6.81   0.00    6.81
annotateU12     5.47   0.15    5.63
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/IntEREst.Rcheck/00check.log'
for details.



Installation output

IntEREst.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/IntEREst_1.14.0.tar.gz && rm -rf IntEREst.buildbin-libdir && mkdir IntEREst.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IntEREst.buildbin-libdir IntEREst_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL IntEREst_1.14.0.zip && rm IntEREst_1.14.0.tar.gz IntEREst_1.14.0.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  961k  100  961k    0     0  30.6M      0 --:--:-- --:--:-- --:--:-- 31.2M

install for i386

* installing *source* package 'IntEREst' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IntEREst'
    finding HTML links ... done
    DEXSeqIntEREst                          html  
    IntEREst-package                        html  
    addAnnotation                           html  
    annotateU12                             html  
    applyOverlap                            html  
    attributes                              html  
    boxplot-method                          html  
    buildSsTypePwms                         html  
    counts-method                           html  
    deseqInterest                           html  
    exactTestInterest                       html  
    getRepeatTable                          html  
    glmInterest                             html  
    interest                                html  
    interest.sequential                     html  
    interestResult                          html  
    interestResultIntEx                     html  
    intexIndex                              html  
    lfc                                     html  
    mdsChr22ExObj                           html  
    mdsChr22IntSpObj                        html  
    mdsChr22Obj                             html  
    mergeInterestResult                     html  
    plot-method                             html  
    psi                                     html  
    pwmU12db                                html  
    qlfInterest                             html  
    readInterestResults                     html  
    referencePrepare                        html  
    subInterestResult                       html  
    treatInterest                           html  
    u12                                     html  
    u12Boxplot                              html  
    u12BoxplotNb                            html  
    u12DensityPlot                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp23NHlq/R.INSTALL25cc3e7248d4/IntEREst/man/u12DensityPlot.Rd:123: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    u12Index                                html  
    u12NbIndex                              html  
    unionRefTr                              html  
    updateRowDataCol                        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 'IntEREst' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IntEREst' as IntEREst_1.14.0.zip
* DONE (IntEREst)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'IntEREst' successfully unpacked and MD5 sums checked

Tests output


Example timings

IntEREst.Rcheck/examples_i386/IntEREst-Ex.timings

nameusersystemelapsed
DEXSeqIntEREst22.87 0.7223.68
addAnnotation0.030.000.03
annotateU123.160.223.37
applyOverlap0.170.030.20
attributes0.030.000.04
boxplot-method0.050.030.08
buildSsTypePwms000
counts-method0.010.000.02
deseqInterest6.130.146.26
exactTestInterest0.220.000.22
getRepeatTable000
glmInterest0.220.000.21
interest1.330.021.35
interest.sequential1.480.001.48
interestResult0.020.000.02
interestResultIntEx0.140.000.14
intexIndex0.010.000.01
lfc0.270.010.29
mergeInterestResult0.060.000.06
plot-method0.280.000.28
psi0.850.000.84
qlfInterest0.290.000.30
readInterestResults0.050.000.05
referencePrepare1.610.001.61
subInterestResult0.060.000.06
treatInterest0.330.000.33
u12Boxplot0.140.000.14
u12BoxplotNb0.170.000.17
u12DensityPlot1.440.001.44
u12Index0.020.000.01
u12NbIndex0.140.000.14
unionRefTr0.030.000.03
updateRowDataCol0.050.000.05

IntEREst.Rcheck/examples_x64/IntEREst-Ex.timings

nameusersystemelapsed
DEXSeqIntEREst35.20 0.1635.36
addAnnotation0.070.000.06
annotateU125.470.155.63
applyOverlap0.310.000.31
attributes0.070.000.06
boxplot-method0.090.000.09
buildSsTypePwms000
counts-method0.050.000.05
deseqInterest6.810.006.81
exactTestInterest0.110.000.11
getRepeatTable000
glmInterest0.230.000.24
interest2.380.022.39
interest.sequential2.440.002.44
interestResult0.030.000.03
interestResultIntEx0.250.000.25
intexIndex0.020.000.02
lfc0.370.000.37
mergeInterestResult0.100.020.11
plot-method0.530.000.53
psi1.360.001.36
qlfInterest0.360.000.36
readInterestResults0.050.000.05
referencePrepare1.800.011.81
subInterestResult0.040.000.05
treatInterest0.300.000.29
u12Boxplot0.140.000.14
u12BoxplotNb0.220.000.22
u12DensityPlot0.50.00.5
u12Index0.010.000.01
u12NbIndex0.160.000.16
unionRefTr0.030.000.03
updateRowDataCol0.060.000.06