Package: GSCA

Version: 2.13.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GSCA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GSCA_2.13.0.tar.gz

StartedAt: 2019-04-09 01:05:04 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:08:44 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 220.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSCA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GSCA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GSCA_2.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GSCA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSCA’ version ‘2.13.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'shiny', 'sp', 'gplots', 'ggplot2', 'reshape2', 'RColorBrewer',
  'rhdf5'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GSCA’ can be installed ... 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘Affyhgu133A2Expr’ ‘Affyhgu133Plus2Expr’ ‘Affyhgu133aExpr’
  ‘Affymoe4302Expr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSCA: no visible global function definition for ‘data’
GSCA: no visible binding for global variable ‘Affyhgu133aExprtab’
GSCA: no visible binding for global variable ‘Affymoe4302Exprtab’
GSCA: no visible binding for global variable ‘Affyhgu133A2Exprtab’
GSCA: no visible binding for global variable ‘Affyhgu133Plus2Exprtab’
GSCA: no visible binding for global variable ‘geneid’
GSCA: no visible global function definition for ‘qnorm’
GSCA: no visible global function definition for ‘sd’
GSCA: no visible global function definition for ‘quantile’
GSCA: no visible global function definition for ‘fisher.test’
GSCAeda: no visible global function definition for ‘data’
GSCAeda: no visible binding for global variable ‘Affyhgu133aExprtab’
GSCAeda: no visible binding for global variable ‘Affymoe4302Exprtab’
GSCAeda: no visible binding for global variable ‘Affyhgu133A2Exprtab’
GSCAeda: no visible binding for global variable
  ‘Affyhgu133Plus2Exprtab’
GSCAeda: no visible binding for global variable ‘geneid’
GSCAeda: no visible global function definition for ‘qnorm’
GSCAeda: no visible global function definition for ‘sd’
GSCAeda: no visible global function definition for ‘quantile’
GSCAeda: no visible global function definition for ‘pdf’
GSCAeda: no visible global function definition for ‘str’
GSCAeda: no visible binding for global variable ‘variable’
GSCAeda: no visible binding for global variable ‘value’
GSCAeda: no visible binding for global variable ‘SampleType’
GSCAeda: no visible global function definition for ‘par’
GSCAeda: no visible global function definition for ‘colorRampPalette’
GSCAeda: no visible global function definition for ‘t.test’
GSCAeda: no visible binding for global variable ‘Var1’
GSCAeda: no visible binding for global variable ‘Var2’
GSCAeda: no visible binding for global variable ‘t.stat’
GSCAeda: no visible binding for global variable ‘P.value’
GSCAeda: no visible global function definition for ‘fisher.test’
GSCAeda: no visible global function definition for ‘dev.off’
GSCAeda: no visible global function definition for ‘write.csv’
GSCAeda: no visible global function definition for ‘write.table’
GSCAplot: no visible global function definition for ‘data’
GSCAplot: no visible binding for global variable ‘Affyhgu133aExprtab’
GSCAplot: no visible binding for global variable ‘Affymoe4302Exprtab’
GSCAplot: no visible binding for global variable ‘Affyhgu133A2Exprtab’
GSCAplot: no visible binding for global variable
  ‘Affyhgu133Plus2Exprtab’
GSCAplot: no visible global function definition for ‘pdf’
GSCAplot: no visible global function definition for ‘par’
GSCAplot: no visible global function definition for ‘hist’
GSCAplot: no visible global function definition for ‘title’
GSCAplot: no visible global function definition for ‘dev.off’
annotatePeaks: no visible binding for global variable ‘allreffile’
tabSearch: no visible global function definition for ‘data’
tabSearch: no visible binding for global variable ‘Affyhgu133aExprtab’
tabSearch: no visible binding for global variable ‘Affymoe4302Exprtab’
tabSearch: no visible binding for global variable ‘Affyhgu133A2Exprtab’
tabSearch: no visible binding for global variable
  ‘Affyhgu133Plus2Exprtab’
Undefined global functions or variables:
  Affyhgu133A2Exprtab Affyhgu133Plus2Exprtab Affyhgu133aExprtab
  Affymoe4302Exprtab P.value SampleType Var1 Var2 allreffile
  colorRampPalette data dev.off fisher.test geneid hist par pdf qnorm
  quantile sd str t.stat t.test title value variable write.csv
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "fisher.test", "qnorm", "quantile", "sd", "t.test")
  importFrom("utils", "data", "str", "write.csv", "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 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
GSCA          101.597  2.804 116.489
GSCAplot       33.368  1.088  34.672
ConstructTG     7.255  0.040   7.397
GSCAeda         6.772  0.028   7.692
annotatePeaks   6.499  0.068   6.643
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GSCA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GSCA
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GSCA’ ...
** using staged installation
** R
** data
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GSCA)

name	user	system	elapsed
ConstructTG	7.255	0.040	7.397
GSCA	101.597	2.804	116.489
GSCAeda	6.772	0.028	7.692
GSCAplot	33.368	1.088	34.672
GSCAui	0	0	0
Oct4ESC_TG	0.000	0.003	0.003
STAT1_TG	0.001	0.000	0.001
annotatePeaks	6.499	0.068	6.643
geneIDdata	0.073	0.000	0.073
tabSearch	0.351	0.008	0.364