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BioC 3.5: CHECK report for SELEX on tokay2

This page was generated on 2017-08-16 13:24:13 -0400 (Wed, 16 Aug 2017).

Package 1194/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SELEX 1.8.0
Harmen Bussemaker
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/SELEX
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SELEX
Version: 1.8.0
Command: rm -rf SELEX.buildbin-libdir SELEX.Rcheck && mkdir SELEX.buildbin-libdir SELEX.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SELEX.buildbin-libdir SELEX_1.8.0.tar.gz >SELEX.Rcheck\00install.out 2>&1 && cp SELEX.Rcheck\00install.out SELEX-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SELEX.buildbin-libdir --install="check:SELEX-install.out" --force-multiarch --no-vignettes --timings SELEX_1.8.0.tar.gz
StartedAt: 2017-08-16 02:47:21 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:50:50 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 209.1 seconds
RetCode: 0
Status:  OK  
CheckDir: SELEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SELEX.buildbin-libdir SELEX.Rcheck && mkdir SELEX.buildbin-libdir SELEX.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SELEX.buildbin-libdir SELEX_1.8.0.tar.gz >SELEX.Rcheck\00install.out 2>&1 && cp SELEX.Rcheck\00install.out SELEX-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SELEX.buildbin-libdir --install="check:SELEX-install.out" --force-multiarch --no-vignettes --timings SELEX_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SELEX.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SELEX/DESCRIPTION' ... OK
* this is package 'SELEX' version '1.8.0'
* 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 'SELEX' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
selex.config: no visible global function definition for 'read.table'
selex.config: no visible global function definition for 'write.table'
selex.counts: no visible global function definition for 'flush.console'
selex.infogain: no visible global function definition for
  'flush.console'
selex.kmax: no visible global function definition for 'flush.console'
selex.loadCountTable: no visible global function definition for
  'flush.console'
selex.mm: no visible global function definition for 'flush.console'
selex.revcomp: no visible global function definition for
  'complete.cases'
Undefined global functions or variables:
  complete.cases flush.console read.table write.table
Consider adding
  importFrom("stats", "complete.cases")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SELEX           13.25   5.78   18.86
selex.seqfilter  3.64   2.77    6.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SELEX           41.21   6.41   16.74
selex.seqfilter 16.64   2.42    5.58
* 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-3.5-bioc/meat/SELEX.Rcheck/00check.log'
for details.


SELEX.Rcheck/00install.out:


install for i386

* installing *source* package 'SELEX' ...
** 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 'SELEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SELEX' as SELEX_1.8.0.zip
* DONE (SELEX)

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

nameusersystemelapsed
SELEX13.25 5.7818.86
selex.affinities1.020.401.31
selex.config0.170.090.23
selex.countSummary0.990.091.05
selex.counts1.230.301.45
selex.defineSample0.110.110.22
selex.exampledata0.140.090.20
selex.fastqPSFM0.560.110.66
selex.getAttributes0.270.060.31
selex.getRound00.260.050.31
selex.getSeqfilter0.120.050.17
selex.infogain1.390.451.80
selex.infogainSummary0.560.200.76
selex.jvmStatus0.160.080.22
selex.kmax1.390.882.27
selex.kmerPSFM0.440.150.58
selex.loadAnnotation0.190.080.25
selex.mm0.310.270.57
selex.mmProb0.470.220.68
selex.mmSummary0.640.290.89
selex.revcomp0.940.271.20
selex.run1.260.461.71
selex.sample0.130.060.19
selex.samplePSFM0.260.130.36
selex.sampleSummary0.170.070.25
selex.saveAnnotation0.110.080.20
selex.seqfilter3.642.776.49
selex.setwd0.100.030.12
selex.split0.310.220.53
selex.summary1.340.511.83

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

nameusersystemelapsed
SELEX41.21 6.4116.74
selex.affinities0.950.250.86
selex.config0.240.090.19
selex.countSummary1.480.270.89
selex.counts1.860.321.12
selex.defineSample0.030.070.10
selex.exampledata0.250.060.26
selex.fastqPSFM1.140.110.54
selex.getAttributes0.410.110.23
selex.getRound00.170.150.28
selex.getSeqfilter0.570.100.14
selex.infogain2.540.541.20
selex.infogainSummary0.600.180.57
selex.jvmStatus0.060.070.12
selex.kmax1.310.931.75
selex.kmerPSFM0.670.220.58
selex.loadAnnotation0.550.090.30
selex.mm1.120.200.50
selex.mmProb0.660.210.58
selex.mmSummary0.490.150.48
selex.revcomp1.460.201.05
selex.run2.220.651.43
selex.sample0.300.090.19
selex.samplePSFM0.560.090.44
selex.sampleSummary0.170.110.21
selex.saveAnnotation0.060.080.14
selex.seqfilter16.64 2.42 5.58
selex.setwd0.110.050.10
selex.split0.850.250.56
selex.summary1.210.471.43