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CHECK report for ACE on tokay1

This page was generated on 2020-08-09 12:14:55 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ACE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 12/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ACE 1.7.0
Jos B Poell
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/ACE
Branch: master
Last Commit: f89d2ab
Last Changed Date: 2020-04-27 15:18:09 -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: ACE
Version: 1.7.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ACE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ACE_1.7.0.tar.gz
StartedAt: 2020-08-09 04:38:25 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 04:42:43 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 257.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ACE.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:ACE.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ACE_1.7.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ACE.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 'ACE/DESCRIPTION' ... OK
* this is package 'ACE' version '1.7.0'
* 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 'ACE' 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 ... NOTE
Unexported object imported by a ':::' call: 'QDNAseq:::sdDiffTrim'
  See the note in ?`:::` about the use of this operator.
* 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
squaremodel        9.26   0.00    9.26
squaremodelsummary 7.72   0.01    7.73
twosamplecompare   7.25   0.03    7.28
loopsquaremodel    4.94   0.25    5.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
squaremodel        11.48   0.01   11.50
squaremodelsummary 10.38   0.04   10.40
twosamplecompare    7.16   0.01    7.17
loopsquaremodel     6.25   0.05    6.29
* 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-3.12-bioc/meat/ACE.Rcheck/00check.log'
for details.



Installation output

ACE.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/ACE_1.7.0.tar.gz && rm -rf ACE.buildbin-libdir && mkdir ACE.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ACE.buildbin-libdir ACE_1.7.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ACE_1.7.0.zip && rm ACE_1.7.0.tar.gz ACE_1.7.0.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  163k  100  163k    0     0  3928k      0 --:--:-- --:--:-- --:--:-- 4297k

install for i386

* installing *source* package 'ACE' ...
** 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 'ACE'
    finding HTML links ... done
    ACE-package                             html  
    ACEcall                                 html  
    analyzegenomiclocations                 html  
    compresstemplate                        html  
    copyNumbersSegmented                    html  
    correlationmatrix                       html  
    forcesegmentsontemplate                 html  
    getadjustedsegments                     html  
    linkvariants                            html  
    loopsquaremodel                         html  
    objectsampletotemplate                  html  
    postanalysisloop                        html  
    runACE                                  html  
    segmentstotemplate                      html  
    singlemodel                             html  
    singleplot                              html  
    squaremodel                             html  
    squaremodelsummary                      html  
    templatefromequalsegments               html  
    twosamplecompare                        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 'ACE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ACE' as ACE_1.7.0.zip
* DONE (ACE)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ACE' successfully unpacked and MD5 sums checked

Tests output


Example timings

ACE.Rcheck/examples_i386/ACE-Ex.timings

nameusersystemelapsed
ACEcall1.860.071.93
analyzegenomiclocations0.010.000.02
compresstemplate0.040.020.06
copyNumbersSegmented1.130.171.29
correlationmatrix0.170.020.19
forcesegmentsontemplate0.450.000.46
getadjustedsegments0.190.010.20
linkvariants0.030.000.03
loopsquaremodel4.940.255.19
objectsampletotemplate000
postanalysisloop000
runACE000
singlemodel0.950.000.96
singleplot1.190.021.20
squaremodel9.260.009.26
squaremodelsummary7.720.017.73
templatefromequalsegments0.040.000.05
twosamplecompare7.250.037.28

ACE.Rcheck/examples_x64/ACE-Ex.timings

nameusersystemelapsed
ACEcall2.040.172.22
analyzegenomiclocations0.030.000.03
compresstemplate0.060.040.10
copyNumbersSegmented1.350.181.53
correlationmatrix0.20.00.2
forcesegmentsontemplate0.70.00.7
getadjustedsegments0.340.000.34
linkvariants0.040.000.05
loopsquaremodel6.250.056.29
objectsampletotemplate000
postanalysisloop000
runACE000
singlemodel1.160.031.19
singleplot1.780.051.83
squaremodel11.48 0.0111.50
squaremodelsummary10.38 0.0410.40
templatefromequalsegments0.040.000.05
twosamplecompare7.160.017.17