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BioC 3.4: CHECK report for GSCA on moscato1

This page was generated on 2016-09-21 03:45:33 -0700 (Wed, 21 Sep 2016).

Package 550/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 2.3.0
Zhicheng Ji
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSCA
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSCA
Version: 2.3.0
Command: rm -rf GSCA.buildbin-libdir GSCA.Rcheck && mkdir GSCA.buildbin-libdir GSCA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSCA.buildbin-libdir GSCA_2.3.0.tar.gz >GSCA.Rcheck\00install.out 2>&1 && cp GSCA.Rcheck\00install.out GSCA-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GSCA.buildbin-libdir --install="check:GSCA-install.out" --force-multiarch --no-vignettes --timings GSCA_2.3.0.tar.gz
StartedAt: 2016-09-20 10:04:44 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:13:11 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 507.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GSCA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GSCA.buildbin-libdir GSCA.Rcheck && mkdir GSCA.buildbin-libdir GSCA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSCA.buildbin-libdir GSCA_2.3.0.tar.gz >GSCA.Rcheck\00install.out 2>&1 && cp GSCA.Rcheck\00install.out GSCA-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GSCA.buildbin-libdir --install="check:GSCA-install.out" --force-multiarch --no-vignettes --timings GSCA_2.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GSCA.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.3.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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          94.95   2.21  125.94
ConstructTG   40.45   0.02   40.48
annotatePeaks 36.17   0.22   36.40
GSCAplot      25.03   0.70   25.78
GSCAeda        4.60   0.04    5.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
GSCA          88.73   2.01   97.49
ConstructTG   35.15   0.02   35.30
annotatePeaks 31.68   0.16   31.84
GSCAplot      25.86   0.73   26.60
GSCAeda        5.15   0.08    6.18
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/GSCA.Rcheck/00check.log'
for details.


GSCA.Rcheck/00install.out:


install for i386

* installing *source* package 'GSCA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GSCA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSCA' as GSCA_2.3.0.zip
* DONE (GSCA)

GSCA.Rcheck/examples_i386/GSCA-Ex.timings:

nameusersystemelapsed
ConstructTG40.45 0.0240.48
GSCA 94.95 2.21125.94
GSCAeda4.600.045.68
GSCAplot25.03 0.7025.78
GSCAui000
Oct4ESC_TG000
STAT1_TG0.000.010.02
annotatePeaks36.17 0.2236.40
geneIDdata0.080.000.07
tabSearch0.330.000.33

GSCA.Rcheck/examples_x64/GSCA-Ex.timings:

nameusersystemelapsed
ConstructTG35.15 0.0235.30
GSCA88.73 2.0197.49
GSCAeda5.150.086.18
GSCAplot25.86 0.7326.60
GSCAui000
Oct4ESC_TG000
STAT1_TG000
annotatePeaks31.68 0.1631.84
geneIDdata0.050.000.05
tabSearch0.270.030.29