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This page was generated on 2021-10-21 12:05:01 -0400 (Thu, 21 Oct 2021).

CHECK results for REDseq on riesling1

To the developers/maintainers of the REDseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/REDseq.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 1565/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.39.0  (landing page)
Lihua Julie Zhu
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/REDseq
git_branch: master
git_last_commit: 515e072
git_last_commit_date: 2021-05-19 11:48:43 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: REDseq
Version: 1.39.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings REDseq_1.39.0.tar.gz
StartedAt: 2021-10-21 03:33:01 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 03:37:41 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 280.6 seconds
RetCode: 0
Status:   OK  
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings REDseq_1.39.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/REDseq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'REDseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REDseq' version '1.39.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'BSgenome.Celegans.UCSC.ce2', 'multtest',
  'Biostrings', 'BSgenome', 'ChIPpeakAnno'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'REDseq' 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 ... NOTE
buildREmap: no visible global function definition for 'start<-'
Undefined global functions or variables:
  start<-
* 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
** 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
  'D:/biocbuild/bbs-3.14-bioc/meat/REDseq.Rcheck/00check.log'
for details.



Installation output

REDseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/REDseq_1.39.0.tar.gz && rm -rf REDseq.buildbin-libdir && mkdir REDseq.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=REDseq.buildbin-libdir REDseq_1.39.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL REDseq_1.39.0.zip && rm REDseq_1.39.0.tar.gz REDseq_1.39.0.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 30798  100 30798    0     0   261k      0 --:--:-- --:--:-- --:--:--  261k

install for i386

* installing *source* package 'REDseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** help
*** installing help indices
  converting help for package 'REDseq'
    finding HTML links ... done
    REDseq-package                          html  
    assignSeq2REsite                        html  
    binom.test.REDseq                       html  
    buildREmap                              html  
    compareREDseq                           html  
    distanceHistSeq2RE                      html  
    example.REDseq                          html  
    example.assignedREDseq                  html  
    example.map                             html  
    plotCutDistribution                     html  
    searchPattern                           html  
    summarizeByRE                           html  
    summarizeBySeq                          html  
    writeHits                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'REDseq' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
* MD5 sums
packaged installation of 'REDseq' as REDseq_1.39.0.zip
* DONE (REDseq)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'REDseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

REDseq.Rcheck/examples_i386/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package000
assignSeq2REsite0.150.000.16
binom.test.REDseq000
buildREmap4.140.114.25
compareREDseq0.010.000.01
distanceHistSeq2RE0.020.000.02
example.REDseq0.000.010.01
example.assignedREDseq000
example.map000
plotCutDistribution0.000.020.02
searchPattern3.080.143.22
summarizeByRE000
summarizeBySeq0.000.020.01
writeHits000

REDseq.Rcheck/examples_x64/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package000
assignSeq2REsite0.170.020.18
binom.test.REDseq000
buildREmap4.340.044.41
compareREDseq0.020.000.01
distanceHistSeq2RE0.010.000.02
example.REDseq000
example.assignedREDseq0.020.000.01
example.map000
plotCutDistribution0.010.000.02
searchPattern3.190.053.23
summarizeByRE000
summarizeBySeq0.020.000.02
writeHits000