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CHECK report for clusterSeq on tokay1

This page was generated on 2019-04-13 11:27:23 -0400 (Sat, 13 Apr 2019).

Package 280/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterSeq 1.6.0
Thomas J. Hardcastle
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/clusterSeq
Branch: RELEASE_3_8
Last Commit: bc978ee
Last Changed Date: 2018-10-30 11:42:03 -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 [ WARNINGS ] 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: clusterSeq
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings clusterSeq_1.6.0.tar.gz
StartedAt: 2019-04-13 01:18:12 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:35:55 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 1062.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clusterSeq.Rcheck
Warnings: 1

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:clusterSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings clusterSeq_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/clusterSeq.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 'clusterSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clusterSeq' version '1.6.0'
* 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'
 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-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/associatePosteriors.Rd:19: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/associatePosteriors.Rd:33: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/cD.ratThymus-data.Rd:9: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/cD.ratThymus-data.Rd:19: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/cD.ratThymus-data.Rd:17: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/kCluster.Rd:20: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/kCluster.Rd:70: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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
* 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 ... 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
makeClustersFF      6.32   0.06   60.80
kCluster            1.26   0.25  119.53
clusterSeq-package  1.03   0.20   89.53
wallace             1.03   0.01   64.44
plotCluster         0.66   0.02   16.40
makeClusters        0.46   0.14   68.14
associatePosteriors 0.33   0.02   15.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
makeClustersFF      5.25   0.06   57.15
clusterSeq-package  1.40   0.11   85.31
kCluster            1.19   0.27  137.95
wallace             1.14   0.11   68.00
makeClusters        0.92   0.17   80.30
plotCluster         0.44   0.05   14.08
associatePosteriors 0.25   0.01   15.92
* 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-3.8-bioc/meat/clusterSeq.Rcheck/00check.log'
for details.



Installation output

clusterSeq.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/clusterSeq_1.6.0.tar.gz && rm -rf clusterSeq.buildbin-libdir && mkdir clusterSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterSeq.buildbin-libdir clusterSeq_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL clusterSeq_1.6.0.zip && rm clusterSeq_1.6.0.tar.gz clusterSeq_1.6.0.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  846k  100  846k    0     0  3943k      0 --:--:-- --:--:-- --:--:-- 4030k

install for i386

* installing *source* package 'clusterSeq' ...
** R
** data
** byte-compile and prepare 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-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/associatePosteriors.Rd:19: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/associatePosteriors.Rd:33: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
    cD.ratThymus-data                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/cD.ratThymus-data.Rd:9: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/cD.ratThymus-data.Rd:19: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/cD.ratThymus-data.Rd:17: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
    clusterSeq-package                      html  
    kCluster                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/kCluster.Rd:20: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpmqlUPf/R.INSTALL1e185fc34fd8/clusterSeq/man/kCluster.Rd:70: file link 'countData' in package 'baySeq' does not exist and so has been treated as a topic
    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_1.6.0.zip
* DONE (clusterSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'clusterSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

clusterSeq.Rcheck/examples_i386/clusterSeq-Ex.timings

nameusersystemelapsed
associatePosteriors 0.33 0.0215.61
clusterSeq-package 1.03 0.2089.53
kCluster 1.26 0.25119.53
makeClusters 0.46 0.1468.14
makeClustersFF 6.32 0.0660.80
plotCluster 0.66 0.0216.40
wallace 1.03 0.0164.44

clusterSeq.Rcheck/examples_x64/clusterSeq-Ex.timings

nameusersystemelapsed
associatePosteriors 0.25 0.0115.92
clusterSeq-package 1.40 0.1185.31
kCluster 1.19 0.27137.95
makeClusters 0.92 0.1780.30
makeClustersFF 5.25 0.0657.15
plotCluster 0.44 0.0514.08
wallace 1.14 0.1168.00