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CHECK report for anota2seq on tokay1

This page was generated on 2020-08-13 11:42:56 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE anota2seq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 67/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
anota2seq 1.11.0
Christian Oertlin , Julie Lorent
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/anota2seq
Branch: master
Last Commit: 0e34b88
Last Changed Date: 2020-04-27 15:11:14 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: anota2seq
Version: 1.11.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:anota2seq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings anota2seq_1.11.0.tar.gz
StartedAt: 2020-08-13 04:29:56 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 04:37:52 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 475.4 seconds
RetCode: 0
Status:  OK  
CheckDir: anota2seq.Rcheck
Warnings: 0

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:anota2seq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings anota2seq_1.11.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/anota2seq.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'anota2seq/DESCRIPTION' ... OK
* this is package 'anota2seq' version '1.11.0'
* 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 'anota2seq' 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 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
anota2seqGetResidOutlierTest 42.94   0.06   43.01
anota2seqGetQualityControl   40.41   0.60   41.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
anota2seqGetResidOutlierTest 50.73   0.06   50.80
anota2seqGetQualityControl   41.10   0.05   41.14
anota2seqAnalyze              1.73   0.05    5.87
* 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

anota2seq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/anota2seq_1.11.0.tar.gz && rm -rf anota2seq.buildbin-libdir && mkdir anota2seq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=anota2seq.buildbin-libdir anota2seq_1.11.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL anota2seq_1.11.0.zip && rm anota2seq_1.11.0.tar.gz anota2seq_1.11.0.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  510k  100  510k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.4M

install for i386

* installing *source* package 'anota2seq' ...
** 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 'anota2seq'
    finding HTML links ... done
    Anota2seqDataSet-class                  html  
    anota2seq-plots                         html  
    anota2seqAnalyze                        html  
    anota2seqDataSetFromMatrix              html  
    anota2seqGetContrasts                   html  
    anota2seqGetCovariates                  html  
    anota2seqGetDeltaData                   html  
    anota2seqGetNormalizedData              html  
    anota2seqGetOutput                      html  
    anota2seqGetQualityControl              html  
    anota2seqGetResidOutlierTest            html  
    anota2seqGetThresholds                  html  
    anota2seqPerformQC                      html  
    anota2seqRegModes                       html  
    anota2seqResidOutlierTest               html  
    anota2seqRun                            html  
    anota2seqSelSigGenes                    html  
    anota2seq_data                          html  
    show-Anota2seqDataSet-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 'anota2seq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'anota2seq' as anota2seq_1.11.0.zip
* DONE (anota2seq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'anota2seq' successfully unpacked and MD5 sums checked

Tests output


Example timings

anota2seq.Rcheck/examples_i386/anota2seq-Ex.timings

nameusersystemelapsed
anota2seq-plots000
anota2seqAnalyze0.850.051.00
anota2seqDataSetFromMatrix0.080.010.10
anota2seqGetContrasts0.710.020.73
anota2seqGetCovariates0.570.000.57
anota2seqGetDeltaData0.570.030.60
anota2seqGetNormalizedData0.050.000.05
anota2seqGetOutput0.560.000.56
anota2seqGetQualityControl40.41 0.6041.07
anota2seqGetResidOutlierTest42.94 0.0643.01
anota2seqGetThresholds0.870.000.88
anota2seqPerformQC000
anota2seqRegModes2.350.062.40
anota2seqResidOutlierTest000
anota2seqRun2.140.022.16
anota2seqSelSigGenes0.680.030.72
anota2seq_data0.040.000.03
show-Anota2seqDataSet-method0.120.000.12

anota2seq.Rcheck/examples_x64/anota2seq-Ex.timings

nameusersystemelapsed
anota2seq-plots000
anota2seqAnalyze1.730.055.87
anota2seqDataSetFromMatrix0.070.010.09
anota2seqGetContrasts0.690.030.72
anota2seqGetCovariates0.980.000.98
anota2seqGetDeltaData0.600.000.59
anota2seqGetNormalizedData0.010.020.03
anota2seqGetOutput0.540.010.56
anota2seqGetQualityControl41.10 0.0541.14
anota2seqGetResidOutlierTest50.73 0.0650.80
anota2seqGetThresholds0.660.000.65
anota2seqPerformQC000
anota2seqRegModes1.940.062.00
anota2seqResidOutlierTest000
anota2seqRun2.120.072.19
anota2seqSelSigGenes1.530.031.56
anota2seq_data0.020.010.03
show-Anota2seqDataSet-method0.110.000.11