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CHECK report for iGC on tokay2

This page was generated on 2019-10-16 12:33:57 -0400 (Wed, 16 Oct 2019).

Package 798/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iGC 1.14.0
Liang-Bo Wang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/iGC
Branch: RELEASE_3_9
Last Commit: b4c09bd
Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iGC
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iGC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iGC_1.14.0.tar.gz
StartedAt: 2019-10-16 04:31:45 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:32:37 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 52.0 seconds
RetCode: 0
Status:  OK  
CheckDir: iGC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iGC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings iGC_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/iGC.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iGC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iGC' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 '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
* 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
* 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 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 : : no visible binding for global variable
  'GENE'
direct_gene_cna : : 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 : : no
  visible global function definition for 'na.omit'
find_cna_driven_gene : exp_grouptest_driven_by_cna : : 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/iGC.Rcheck/00check.log'
for details.



Installation output

iGC.Rcheck/00install.out

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### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/iGC_1.14.0.tar.gz && rm -rf iGC.buildbin-libdir && mkdir iGC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iGC.buildbin-libdir iGC_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL iGC_1.14.0.zip && rm iGC_1.14.0.tar.gz iGC_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2781k  100 2781k    0     0  14.1M      0 --:--:-- --:--:-- --:--:-- 14.6M

install for i386

* installing *source* package 'iGC' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'iGC'
    finding HTML links ... done
    create_gene_cna                         html  
    create_gene_exp                         html  
    create_sample_desc                      html  
    direct_gene_cna                         html  
    find_cna_driven_gene                    html  
    hg19DBNM                                html  
    iGC                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'iGC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iGC' as iGC_1.14.0.zip
* DONE (iGC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'iGC' successfully unpacked and MD5 sums checked

Tests output


Example timings

iGC.Rcheck/examples_i386/iGC-Ex.timings

nameusersystemelapsed
create_gene_cna1.380.362.33
create_gene_exp0.090.001.28
create_sample_desc000
direct_gene_cna0.040.000.04
find_cna_driven_gene0.050.060.08

iGC.Rcheck/examples_x64/iGC-Ex.timings

nameusersystemelapsed
create_gene_cna1.380.362.00
create_gene_exp0.090.000.10
create_sample_desc000
direct_gene_cna0.040.000.05
find_cna_driven_gene0.080.020.09