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BioC 3.4: CHECK report for iGC on zin1

This page was generated on 2016-09-21 03:40:10 -0700 (Wed, 21 Sep 2016).

Package 605/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iGC 1.3.2
Liang-Bo Wang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iGC
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iGC
Version: 1.3.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iGC_1.3.2.tar.gz
StartedAt: 2016-09-20 08:04:46 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:05:06 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 20.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iGC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iGC_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/iGC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iGC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iGC’ version ‘1.3.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘iGC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
create_gene_cna: no visible global function definition for ‘data’
create_gene_cna: no visible binding for global variable ‘hg19DBNM’
create_gene_cna: no visible binding for global variable ‘Gene.Symbol’
create_gene_cna: no visible binding for global variable ‘GENE’
direct_gene_cna : <anonymous>: no visible binding for global variable
  ‘GENE’
direct_gene_cna : <anonymous>: no visible binding for global variable
  ‘gain_loss’
direct_gene_cna: no visible binding for global variable ‘GENE’
find_cna_driven_gene: no visible binding for global variable ‘GENE’
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding
  for global variable ‘Gain’
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding
  for global variable ‘GENE’
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible binding
  for global variable ‘Loss’
find_cna_driven_gene : exp_grouptest_driven_by_cna : <anonymous>: no
  visible global function definition for ‘na.omit’
find_cna_driven_gene : exp_grouptest_driven_by_cna : <anonymous>: no
  visible global function definition for ‘t.test’
find_cna_driven_gene : exp_grouptest_driven_by_cna: no visible global
  function definition for ‘p.adjust’
find_cna_driven_gene: no visible binding for global variable ‘p_value’
find_cna_driven_gene: no visible binding for global variable ‘fdr’
find_cna_driven_gene: no visible binding for global variable
  ‘vs_rest_exp_diff’
process_cna_per_sample: no visible binding for global variable
  ‘gain_loss’
process_cna_per_sample: no visible binding for global variable
  ‘Segment_Mean’
process_cna_per_sample: no visible binding for global variable
  ‘Chromosome’
process_cna_per_sample: no visible binding for global variable ‘Start’
process_cna_per_sample: no visible binding for global variable ‘End’
process_cna_per_sample: no visible binding for global variable
  ‘Gene.Symbol’
process_cna_per_sample: no visible binding for global variable
  ‘cur_sample’
process_cna_per_sample_direct: no visible binding for global variable
  ‘Segment_Mean’
process_cna_per_sample_direct: no visible binding for global variable
  ‘gain_loss’
process_cna_per_sample_direct: no visible binding for global variable
  ‘cna_val’
read_cna_geo: no visible binding for global variable ‘GENE’
read_cna_geo: no visible binding for global variable ‘Segment_Mean’
read_gene_exp: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  Chromosome End GENE Gain Gene.Symbol Loss Segment_Mean Start cna_val
  cur_sample data fdr gain_loss hg19DBNM na.omit p.adjust p_value
  read.table t.test vs_rest_exp_diff
Consider adding
  importFrom("stats", "na.omit", "p.adjust", "t.test")
  importFrom("utils", "data", "read.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 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 ... 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-3.4-bioc/meat/iGC.Rcheck/00check.log’
for details.


iGC.Rcheck/00install.out:

* installing *source* package ‘iGC’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iGC)

iGC.Rcheck/iGC-Ex.timings:

nameusersystemelapsed
create_gene_cna1.4080.0081.417
create_gene_exp0.0760.0000.075
create_sample_desc0.0080.0000.006
direct_gene_cna0.0200.0000.022
find_cna_driven_gene0.0480.0000.048