Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:19 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ChIPsim on tokay2


To the developers/maintainers of the ChIPsim package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPsim.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 307/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPsim 1.48.0  (landing page)
Peter Humburg
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/ChIPsim
git_branch: RELEASE_3_14
git_last_commit: 5b9f34f
git_last_commit_date: 2021-10-26 11:54:24 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPsim
Version: 1.48.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPsim_1.48.0.tar.gz
StartedAt: 2022-04-12 17:14:06 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:18:10 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 244.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPsim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChIPsim_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPsim.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPsim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPsim' version '1.48.0'
* 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 'ChIPsim' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biostrings'
A package should be listed in only one of these fields.
* 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 ... NOTE
print.SimulatedFeature: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChIPsim.Rcheck/00check.log'
for details.



Installation output

ChIPsim.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ChIPsim_1.48.0.tar.gz && rm -rf ChIPsim.buildbin-libdir && mkdir ChIPsim.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPsim.buildbin-libdir ChIPsim_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ChIPsim_1.48.0.zip && rm ChIPsim_1.48.0.tar.gz ChIPsim_1.48.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 40 39295   40 16067    0     0   136k      0 --:--:-- --:--:-- --:--:--  136k
100 39295  100 39295    0     0    97k      0 --:--:-- --:--:-- --:--:-- 99987

install for i386

* installing *source* package 'ChIPsim' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPsim'
    finding HTML links ... done
    ChIPsim-package                         html  
    bindDens2readDens                       html  
    decodeQuality                           html  
    defaultControl                          html  
    defaultErrorProb                        html  
    defaultFunctions                        html  
    defaultGenerator                        html  
    distDens                                html  
    extractQuality                          html  
    feat2dens                               html  
    featureDensity                          html  
    internal                                html  
    joinRegion                              html  
    makeFeatures                            html  
    placeFeatures                           html  
    pos2fastq                               html  
    readError                               html  
    readQualitySample                       html  
    readSequence                            html  
    reconcileFeatures                       html  
    sampleReads                             html  
    simChIP                                 html  
    simpleNames                             html  
    stableFeature                           html  
    writeFASTQ                              html  
    writeReads                              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 'ChIPsim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPsim' as ChIPsim_1.48.0.zip
* DONE (ChIPsim)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ChIPsim' successfully unpacked and MD5 sums checked

Tests output


Example timings

ChIPsim.Rcheck/examples_i386/ChIPsim-Ex.timings

nameusersystemelapsed
ChIPsim-package000
bindDens2readDens1.390.101.48
decodeQuality000
defaultControl000
defaultErrorProb000
defaultFunctions000
defaultGenerator0.030.000.03
extractQuality000
feat2dens0.790.000.80
featureDensity000
makeFeatures0.050.000.05
placeFeatures0.060.000.06
pos2fastq0.050.000.05
readError000
reconcileFeatures0.050.000.05
sampleReads1.330.041.36
simChIP000
simpleNames000
stableFeature0.000.010.02
writeFASTQ000

ChIPsim.Rcheck/examples_x64/ChIPsim-Ex.timings

nameusersystemelapsed
ChIPsim-package000
bindDens2readDens1.530.001.53
decodeQuality000
defaultControl0.010.000.01
defaultErrorProb000
defaultFunctions000
defaultGenerator0.050.000.05
extractQuality000
feat2dens0.80.00.8
featureDensity000
makeFeatures0.040.000.04
placeFeatures0.070.000.07
pos2fastq0.040.020.06
readError000
reconcileFeatures0.070.000.06
sampleReads0.860.000.86
simChIP000
simpleNames000
stableFeature000
writeFASTQ000