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BioC 3.2: CHECK report for rfPred on zin1

This page was generated on 2016-04-23 10:13:14 -0700 (Sat, 23 Apr 2016).

Package 873/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rfPred 1.8.0
Hugo Varet
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rfPred
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rfPred
Version: 1.8.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rfPred_1.8.0.tar.gz
StartedAt: 2016-04-23 04:41:04 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:42:27 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 82.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rfPred.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rfPred_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/rfPred.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rfPred/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rfPred’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rfPred’ can be installed ... [8s/8s] 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
* 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 ... NOTE
'library' or 'require' call to ‘Rsamtools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘IRanges’ ‘Rsamtools’ ‘data.table’ ‘methods’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rfPred_scores_motor: no visible global function definition for
  ‘as.data.table’
rfPred_scores_motor: no visible global function definition for
  ‘IRanges’
rfPred_scores_motor: no visible global function definition for
  ‘scanTabix’
rfPred_scores_motor: no visible global function definition for
  ‘TabixFile’
rfPred_scores_motor: no visible global function definition for
  ‘makeCluster’
rfPred_scores_motor: no visible global function definition for
  ‘parLapply’
rfPred_scores_motor: no visible global function definition for
  ‘clusterSplit’
rfPred_scores_motor : <anonymous>: no visible global function
  definition for ‘scanTabix’
rfPred_scores_motor: no visible global function definition for
  ‘stopCluster’
rfPred_scores,GRanges: no visible global function definition for
  ‘seqlevels<-’
rfPred_scores,GRanges: no visible global function definition for
  ‘seqlevels’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/rfPred.Rcheck/00check.log’
for details.


rfPred.Rcheck/00install.out:

* installing *source* package ‘rfPred’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c outstring.c -o outstring.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o rfPred.so outstring.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/rfPred.Rcheck/rfPred/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rfPred)

rfPred.Rcheck/rfPred-Ex.timings:

nameusersystemelapsed
rfPred_scores-methods0.4770.0080.485