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BioC 3.4: CHECK report for pbcmc on tokay1

This page was generated on 2017-04-15 16:21:03 -0400 (Sat, 15 Apr 2017).

Package 900/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pbcmc 1.2.2
Cristobal Fresno
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/pbcmc
Last Changed Rev: 124567 / Revision: 128728
Last Changed Date: 2016-11-29 12:47:46 -0500 (Tue, 29 Nov 2016)
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 [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pbcmc
Version: 1.2.2
Command: rm -rf pbcmc.buildbin-libdir pbcmc.Rcheck && mkdir pbcmc.buildbin-libdir pbcmc.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pbcmc.buildbin-libdir pbcmc_1.2.2.tar.gz >pbcmc.Rcheck\00install.out 2>&1 && cp pbcmc.Rcheck\00install.out pbcmc-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=pbcmc.buildbin-libdir --install="check:pbcmc-install.out" --force-multiarch --no-vignettes --timings pbcmc_1.2.2.tar.gz
StartedAt: 2017-04-14 23:59:30 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-15 00:06:35 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 424.2 seconds
RetCode: 0
Status:  OK  
CheckDir: pbcmc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf pbcmc.buildbin-libdir pbcmc.Rcheck && mkdir pbcmc.buildbin-libdir pbcmc.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pbcmc.buildbin-libdir pbcmc_1.2.2.tar.gz >pbcmc.Rcheck\00install.out 2>&1 && cp pbcmc.Rcheck\00install.out pbcmc-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=pbcmc.buildbin-libdir --install="check:pbcmc-install.out" --force-multiarch --no-vignettes --timings pbcmc_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/pbcmc.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pbcmc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pbcmc' version '1.2.2'
* 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 'pbcmc' 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 ... 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
PAM50-class                            2.05   0.06   11.75
MolecularPermutationClassifierGenerics 0.19   0.06   19.23
PAM50Permutate                         0.15   0.06   19.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                       user system elapsed
PAM50-class                            2.52   0.11   13.37
MolecularPermutationClassifierGenerics 0.17   0.12   24.61
PAM50Permutate                         0.14   0.06   20.76
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: OK

pbcmc.Rcheck/00install.out:


install for i386

* installing *source* package 'pbcmc' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: unlist
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: unlist

install for x64

* installing *source* package 'pbcmc' ...
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: unlist
* MD5 sums
packaged installation of 'pbcmc' as pbcmc_1.2.2.zip
* DONE (pbcmc)

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

nameusersystemelapsed
MolecularPermutationClassifierConstructor0.920.032.02
MolecularPermutationClassifierGenerics 0.19 0.0619.23
MolecularPermutationClassifierGetseters0.060.000.06
MolecularPermutationClassifierShow0.050.020.06
PAM50-class 2.05 0.0611.75
PAM50Classify0.070.000.08
PAM50Constructor0.710.080.78
PAM50Filtrate1.160.031.19
PAM50Permutate 0.15 0.0619.79
PAM50SubjectReport2.240.072.30
PAM50Subtype0.060.000.06

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

nameusersystemelapsed
MolecularPermutationClassifierConstructor0.920.000.92
MolecularPermutationClassifierGenerics 0.17 0.1224.61
MolecularPermutationClassifierGetseters0.030.030.06
MolecularPermutationClassifierShow0.080.000.08
PAM50-class 2.52 0.1113.37
PAM50Classify0.060.000.07
PAM50Constructor0.980.031.02
PAM50Filtrate1.170.081.25
PAM50Permutate 0.14 0.0620.76
PAM50SubjectReport3.500.023.53
PAM50Subtype0.050.010.06