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This page was generated on 2022-01-14 13:05:59 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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 alsace on tokay2


To the developers/maintainers of the alsace package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alsace.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 47/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.30.0  (landing page)
Ron Wehrens
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/alsace
git_branch: RELEASE_3_14
git_last_commit: d0e09b2
git_last_commit_date: 2021-10-26 12:12:10 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: alsace
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alsace.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings alsace_1.30.0.tar.gz
StartedAt: 2022-01-13 15:19:52 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 15:21:39 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 107.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: alsace.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alsace.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings alsace_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/alsace.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'alsace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'alsace' version '1.30.0'
* 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 'alsace' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/alsace.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 ... NOTE
'library' or 'require' call to 'lattice' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  'stripplot'
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for 'panel.stripplot'
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for 'panel.abline'
Undefined global functions or variables:
  panel.abline panel.stripplot stripplot
* 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
components 9.72   0.03    9.75
teaMerged  5.55   0.00    5.55
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
components 9.21   0.11    9.33
teaMerged  5.43   0.00    5.42
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/alsace.Rcheck/00check.log'
for details.



Installation output

alsace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/alsace_1.30.0.tar.gz && rm -rf alsace.buildbin-libdir && mkdir alsace.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=alsace.buildbin-libdir alsace_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL alsace_1.30.0.zip && rm alsace_1.30.0.tar.gz alsace_1.30.0.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
100 1067k  100 1067k    0     0  2928k      0 --:--:-- --:--:-- --:--:-- 2932k

install for i386

* installing *source* package 'alsace' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'alsace'
    finding HTML links ... done
    alsace-package                          html  
    components                              html  
    correctPeaks                            html  
    correctRT                               html  
    finding level-2 HTML links ... done

    doALS                                   html  
    filterPeaks                             html  
    fitpeaks                                html  
    getAllPeaks                             html  
    getPeakTable                            html  
    opa                                     html  
    preprocess                              html  
    showALSresult                           html  
    tea                                     html  
    teaMerged                               html  
    windows                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'alsace' ...
** testing if installed package can be loaded
Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
  version 3.15
* MD5 sums
packaged installation of 'alsace' as alsace_1.30.0.zip
* DONE (alsace)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'alsace' successfully unpacked and MD5 sums checked

Tests output


Example timings

alsace.Rcheck/examples_i386/alsace-Ex.timings

nameusersystemelapsed
components9.720.039.75
correctPeaks3.730.013.75
correctRT1.840.001.84
doALS4.580.004.58
filterPeaks0.030.020.05
fitpeaks4.580.014.59
getAllPeaks0.030.020.05
getPeakTable1.910.001.90
opa1.170.001.18
preprocess0.120.020.14
showALSresult0.140.000.14
tea0.110.010.12
teaMerged5.550.005.55
windows0.120.030.16

alsace.Rcheck/examples_x64/alsace-Ex.timings

nameusersystemelapsed
components9.210.119.33
correctPeaks404
correctRT2.160.022.17
doALS4.260.014.28
filterPeaks0.020.020.04
fitpeaks3.750.033.78
getAllPeaks0.030.000.03
getPeakTable2.420.022.44
opa1.220.001.21
preprocess0.110.000.11
showALSresult0.170.000.18
tea0.090.030.12
teaMerged5.430.005.42
windows0.090.030.13