Package: iGC

Version: 1.12.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:iGC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings iGC_1.12.0.tar.gz

StartedAt: 2019-04-16 00:45:04 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:45:34 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 29.5 seconds

RetCode: 0

Status:  OK

CheckDir: iGC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:iGC.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings iGC_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/iGC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.0’
* 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 ‘iGC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
create_gene_cna 9.964  0.092   4.315
* 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-3.8-bioc/meat/iGC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL iGC
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘iGC’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iGC)

name	user	system	elapsed
create_gene_cna	9.964	0.092	4.315
create_gene_exp	0.308	0.000	0.207
create_sample_desc	0.008	0.000	0.008
direct_gene_cna	1.680	0.016	0.571
find_cna_driven_gene	4.344	0.012	1.198