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CHECK report for clusterSeq on tokay1

This page was generated on 2018-04-12 13:29:09 -0400 (Thu, 12 Apr 2018).

Package 251/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterSeq 1.2.0
Thomas J. Hardcastle
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/clusterSeq
Branch: RELEASE_3_6
Last Commit: 48032f4
Last Changed Date: 2017-10-30 12:41:24 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterSeq
Version: 1.2.0
Command: rm -rf clusterSeq.buildbin-libdir clusterSeq.Rcheck && mkdir clusterSeq.buildbin-libdir clusterSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterSeq.buildbin-libdir clusterSeq_1.2.0.tar.gz >clusterSeq.Rcheck\00install.out 2>&1 && cp clusterSeq.Rcheck\00install.out clusterSeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=clusterSeq.buildbin-libdir --install="check:clusterSeq-install.out" --force-multiarch --no-vignettes --timings clusterSeq_1.2.0.tar.gz
StartedAt: 2018-04-11 23:00:56 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:17:31 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 994.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clusterSeq.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf clusterSeq.buildbin-libdir clusterSeq.Rcheck && mkdir clusterSeq.buildbin-libdir clusterSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clusterSeq.buildbin-libdir clusterSeq_1.2.0.tar.gz >clusterSeq.Rcheck\00install.out 2>&1 && cp clusterSeq.Rcheck\00install.out clusterSeq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=clusterSeq.buildbin-libdir --install="check:clusterSeq-install.out" --force-multiarch --no-vignettes --timings clusterSeq_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterSeq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clusterSeq' version '1.2.0'
* 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 'clusterSeq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/associatePosteriors.Rd:19: missing file link 'countData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/associatePosteriors.Rd:33: missing file link 'countData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/cD.ratThymus-data.Rd:9: missing file link 'countData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/cD.ratThymus-data.Rd:19: missing file link 'countData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/cD.ratThymus-data.Rd:17: missing file link 'countData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/kCluster.Rd:20: missing file link 'countData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/kCluster.Rd:70: missing file link 'countData'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterSeq.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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeClustersFF      7.94   0.06   61.67
clusterSeq-package  1.59   0.20   76.69
kCluster            1.16   0.13  107.32
wallace             1.03   0.07   57.23
makeClusters        0.68   0.09   65.74
associatePosteriors 0.47   0.03   16.01
plotCluster         0.38   0.03   12.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeClustersFF      8.39   0.02   71.53
clusterSeq-package  2.72   0.22  106.11
kCluster            2.05   0.16  126.25
wallace             1.16   0.08   62.48
associatePosteriors 0.94   0.01   16.61
plotCluster         0.72   0.03   15.11
makeClusters        0.70   0.04   73.85
* 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
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/clusterSeq.Rcheck/00check.log'
for details.



Installation output

clusterSeq.Rcheck/00install.out


install for i386

* installing *source* package 'clusterSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'clusterSeq'
    finding HTML links ... done
    associatePosteriors                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/associatePosteriors.Rd:19: missing file link 'countData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/associatePosteriors.Rd:33: missing file link 'countData'
    cD.ratThymus-data                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/cD.ratThymus-data.Rd:9: missing file link 'countData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/cD.ratThymus-data.Rd:19: missing file link 'countData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/cD.ratThymus-data.Rd:17: missing file link 'countData'
    clusterSeq-package                      html  
    kCluster                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/kCluster.Rd:20: missing file link 'countData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWaK3UX/R.INSTALLc483df87db6/clusterSeq/man/kCluster.Rd:70: missing file link 'countData'
    makeClusters                            html  
    makeClustersFF                          html  
    plotCluster                             html  
    ratThymus-data                          html  
    wallace                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'clusterSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterSeq' as clusterSeq_1.2.0.zip
* DONE (clusterSeq)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

clusterSeq.Rcheck/examples_i386/clusterSeq-Ex.timings

nameusersystemelapsed
associatePosteriors 0.47 0.0316.01
clusterSeq-package 1.59 0.2076.69
kCluster 1.16 0.13107.32
makeClusters 0.68 0.0965.74
makeClustersFF 7.94 0.0661.67
plotCluster 0.38 0.0312.66
wallace 1.03 0.0757.23

clusterSeq.Rcheck/examples_x64/clusterSeq-Ex.timings

nameusersystemelapsed
associatePosteriors 0.94 0.0116.61
clusterSeq-package 2.72 0.22106.11
kCluster 2.05 0.16126.25
makeClusters 0.70 0.0473.85
makeClustersFF 8.39 0.0271.53
plotCluster 0.72 0.0315.11
wallace 1.16 0.0862.48