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CHECK report for GSCA on tokay1

This page was generated on 2019-04-13 11:23:33 -0400 (Sat, 13 Apr 2019).

Package 690/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 2.12.0
Zhicheng Ji
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GSCA
Branch: RELEASE_3_8
Last Commit: dc0593b
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSCA
Version: 2.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GSCA_2.12.0.tar.gz
StartedAt: 2019-04-13 02:55:06 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:01:33 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 387.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GSCA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GSCA_2.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GSCA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSCA' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GSCA          91.09   3.76  113.60
GSCAplot      22.42   1.22   23.65
annotatePeaks  4.98   0.54    5.53
ConstructTG    4.71   0.10    5.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
GSCA     77.86   3.65   81.78
GSCAplot 21.44   2.03   23.47
* 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-3.8-bioc/meat/GSCA.Rcheck/00check.log'
for details.



Installation output

GSCA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GSCA_2.12.0.tar.gz && rm -rf GSCA.buildbin-libdir && mkdir GSCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSCA.buildbin-libdir GSCA_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GSCA_2.12.0.zip && rm GSCA_2.12.0.tar.gz GSCA_2.12.0.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
100 2149k  100 2149k    0     0  7310k      0 --:--:-- --:--:-- --:--:-- 7412k

install for i386

* installing *source* package 'GSCA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSCA'
    finding HTML links ... done
    ConstructTG                             html  
    GSCA-package                            html  
    GSCA                                    html  
    GSCAeda                                 html  
    GSCAplot                                html  
    GSCAui                                  html  
    Oct4ESC_TG                              html  
    STAT1_TG                                html  
    annotatePeaks                           html  
    geneIDdata                              html  
    tabSearch                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GSCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSCA' as GSCA_2.12.0.zip
* DONE (GSCA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GSCA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

GSCA.Rcheck/examples_i386/GSCA-Ex.timings

nameusersystemelapsed
ConstructTG4.710.105.39
GSCA 91.09 3.76113.60
GSCAeda4.550.044.60
GSCAplot22.42 1.2223.65
GSCAui000
Oct4ESC_TG0.000.020.02
STAT1_TG000
annotatePeaks4.980.545.53
geneIDdata0.060.020.07
tabSearch0.240.050.29

GSCA.Rcheck/examples_x64/GSCA-Ex.timings

nameusersystemelapsed
ConstructTG4.370.054.42
GSCA77.86 3.6581.78
GSCAeda4.910.074.97
GSCAplot21.44 2.0323.47
GSCAui000
Oct4ESC_TG000
STAT1_TG000
annotatePeaks3.650.233.89
geneIDdata0.050.000.05
tabSearch0.220.030.25