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CHECK report for GSCA on tokay2

This page was generated on 2019-10-16 12:29:13 -0400 (Wed, 16 Oct 2019).

Package 724/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 2.14.0
Zhicheng Ji
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GSCA
Branch: RELEASE_3_9
Last Commit: 1ec5a90
Last Changed Date: 2019-05-02 11:53:47 -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: GSCA
Version: 2.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GSCA_2.14.0.tar.gz
StartedAt: 2019-10-16 04:16:14 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:22:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 383.6 seconds
RetCode: 0
Status:  OK  
CheckDir: GSCA.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:GSCA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GSCA_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GSCA.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 'GSCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSCA' version '2.14.0'
* 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 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          89.57   3.93  109.52
GSCAplot      30.91   1.59   32.51
annotatePeaks  6.08   0.58    6.65
GSCAeda        5.12   0.12    5.89
ConstructTG    4.39   0.07    8.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GSCA          92.89   4.74  105.55
GSCAplot      21.28   1.23   22.51
GSCAeda        6.19   0.22    6.41
ConstructTG    5.56   0.01    5.57
annotatePeaks  5.17   0.06    5.24
* 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/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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GSCA_2.14.0.tar.gz && rm -rf GSCA.buildbin-libdir && mkdir GSCA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSCA.buildbin-libdir GSCA_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GSCA_2.14.0.zip && rm GSCA_2.14.0.tar.gz GSCA_2.14.0.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
100 2156k  100 2156k    0     0  19.6M      0 --:--:-- --:--:-- --:--:-- 21.0M

install for i386

* installing *source* package 'GSCA' ...
** using staged installation
** 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 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 'GSCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSCA' as GSCA_2.14.0.zip
* DONE (GSCA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GSCA' successfully unpacked and MD5 sums checked

Tests output


Example timings

GSCA.Rcheck/examples_i386/GSCA-Ex.timings

nameusersystemelapsed
ConstructTG4.390.078.73
GSCA 89.57 3.93109.52
GSCAeda5.120.125.89
GSCAplot30.91 1.5932.51
GSCAui000
Oct4ESC_TG0.000.020.02
STAT1_TG000
annotatePeaks6.080.586.65
geneIDdata0.080.010.10
tabSearch0.360.030.39

GSCA.Rcheck/examples_x64/GSCA-Ex.timings

nameusersystemelapsed
ConstructTG5.560.015.57
GSCA 92.89 4.74105.55
GSCAeda6.190.226.41
GSCAplot21.28 1.2322.51
GSCAui000
Oct4ESC_TG000
STAT1_TG0.000.020.01
annotatePeaks5.170.065.24
geneIDdata0.060.000.06
tabSearch0.250.030.28