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BioC 3.1: CHECK report for clonotypeR on moscato2

This page was generated on 2015-10-09 09:30:23 -0700 (Fri, 09 Oct 2015).

Package 176/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clonotypeR 1.6.0
Charles Plessy
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/clonotypeR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clonotypeR
Version: 1.6.0
Command: rm -rf clonotypeR.buildbin-libdir clonotypeR.Rcheck && mkdir clonotypeR.buildbin-libdir clonotypeR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clonotypeR.buildbin-libdir clonotypeR_1.6.0.tar.gz >clonotypeR.Rcheck\00install.out 2>&1 && cp clonotypeR.Rcheck\00install.out clonotypeR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clonotypeR.buildbin-libdir --install="check:clonotypeR-install.out" --force-multiarch --no-vignettes --timings clonotypeR_1.6.0.tar.gz
StartedAt: 2015-10-09 00:27:28 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:28:00 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 32.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clonotypeR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clonotypeR.buildbin-libdir clonotypeR.Rcheck && mkdir clonotypeR.buildbin-libdir clonotypeR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clonotypeR.buildbin-libdir clonotypeR_1.6.0.tar.gz >clonotypeR.Rcheck\00install.out 2>&1 && cp clonotypeR.Rcheck\00install.out clonotypeR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clonotypeR.buildbin-libdir --install="check:clonotypeR-install.out" --force-multiarch --no-vignettes --timings clonotypeR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/clonotypeR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clonotypeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clonotypeR' version '1.6.0'
* 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 'clonotypeR' 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
** 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 ... WARNING
Undocumented code objects:
  'private_clonotypes'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [1s] OK
** running examples for arch 'x64' ... [1s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [1s]
 [1s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [1s]
 [1s] 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: 1 WARNING
See
  'E:/biocbld/bbs-3.1-bioc/meat/clonotypeR.Rcheck/00check.log'
for details.


clonotypeR.Rcheck/00install.out:


install for i386

* installing *source* package 'clonotypeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'clonotypeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clonotypeR' as clonotypeR_1.6.0.zip
* DONE (clonotypeR)

clonotypeR.Rcheck/examples_i386/clonotypeR-Ex.timings:

nameusersystemelapsed
clonotype_table0.010.000.01
clonotyper_extdata0.020.000.02
common_clonotypes0.030.000.03
is_unproductive000
read_clonotypes0.020.000.02
unique_clonotypes0.010.000.01
yassai_identifier0.140.000.14

clonotypeR.Rcheck/examples_x64/clonotypeR-Ex.timings:

nameusersystemelapsed
clonotype_table0.030.020.05
clonotyper_extdata0.020.000.01
common_clonotypes0.040.000.05
is_unproductive000
read_clonotypes0.020.000.01
unique_clonotypes0.030.000.03
yassai_identifier0.200.030.24