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CHECK report for REDseq on tokay1

This page was generated on 2019-04-13 11:21:39 -0400 (Sat, 13 Apr 2019).

Package 1283/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.28.0
Lihua Julie Zhu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/REDseq
Branch: RELEASE_3_8
Last Commit: 6278804
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: REDseq
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings REDseq_1.28.0.tar.gz
StartedAt: 2019-04-13 04:56:57 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:03:12 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 375.2 seconds
RetCode: 0
Status:  OK  
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REDseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings REDseq_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/REDseq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'Biostrings' 'ChIPpeakAnno' 'multtest'
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 ... NOTE
Package in Depends field not imported from: 'BSgenome.Celegans.UCSC.ce2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 or elapsed time > 5s
           user system elapsed
buildREmap 7.26   0.17    7.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
buildREmap 5.66   0.11    5.77
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/REDseq.Rcheck/00check.log'
for details.



Installation output

REDseq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/REDseq_1.28.0.tar.gz && rm -rf REDseq.buildbin-libdir && mkdir REDseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=REDseq.buildbin-libdir REDseq_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL REDseq_1.28.0.zip && rm REDseq_1.28.0.tar.gz REDseq_1.28.0.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 29984  100 29984    0     0   560k      0 --:--:-- --:--:-- --:--:--  610k

install for i386

* installing *source* package 'REDseq' ...
** 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
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
In R CMD INSTALL

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_1.28.0.zip
* DONE (REDseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'REDseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

REDseq.Rcheck/examples_i386/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package000
assignSeq2REsite0.530.160.69
binom.test.REDseq0.020.000.02
buildREmap7.260.177.43
compareREDseq0.020.000.02
distanceHistSeq2RE0.030.020.04
example.REDseq0.000.010.02
example.assignedREDseq0.010.000.01
example.map0.000.020.02
plotCutDistribution0.030.010.05
searchPattern4.270.174.43
summarizeByRE000
summarizeBySeq000
writeHits0.000.020.01

REDseq.Rcheck/examples_x64/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package0.010.000.02
assignSeq2REsite0.670.030.70
binom.test.REDseq0.020.000.01
buildREmap5.660.115.77
compareREDseq0.010.000.01
distanceHistSeq2RE0.020.020.03
example.REDseq000
example.assignedREDseq0.010.000.02
example.map000
plotCutDistribution0.020.010.03
searchPattern3.760.103.86
summarizeByRE000
summarizeBySeq0.000.010.01
writeHits000