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BioC 3.2: CHECK report for GSCA on moscato1

This page was generated on 2016-04-23 10:20:00 -0700 (Sat, 23 Apr 2016).

Package 470/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSCA 1.8.0
Zhicheng Ji
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GSCA
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSCA
Version: 1.8.0
Command: rm -rf GSCA.buildbin-libdir GSCA.Rcheck && mkdir GSCA.buildbin-libdir GSCA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSCA.buildbin-libdir GSCA_1.8.0.tar.gz >GSCA.Rcheck\00install.out 2>&1 && cp GSCA.Rcheck\00install.out GSCA-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GSCA.buildbin-libdir --install="check:GSCA-install.out" --force-multiarch --no-vignettes --timings GSCA_1.8.0.tar.gz
StartedAt: 2016-04-23 03:23:58 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:36:45 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 766.5 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-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSCA.buildbin-libdir GSCA_1.8.0.tar.gz >GSCA.Rcheck\00install.out 2>&1 && cp GSCA.Rcheck\00install.out GSCA-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GSCA.buildbin-libdir --install="check:GSCA-install.out" --force-multiarch --no-vignettes --timings GSCA_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GSCA.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.8.0'
* 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 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'
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 binding for global variable 'variable'
GSCAeda: no visible binding for global variable 'value'
GSCAeda: no visible binding for global variable 'SampleType'
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'
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'
annotatePeaks: no visible binding for global variable 'allreffile'
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'
* 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' ... [390s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
GSCA          154.24   3.43  192.58
ConstructTG    67.77   0.02   67.79
annotatePeaks  54.18   0.25   60.46
GSCAplot       39.73   0.64   40.76
GSCAeda         7.00   0.09   15.12
** running examples for arch 'x64' ... [302s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
GSCA          131.24   3.34  145.24
ConstructTG    52.40   0.05   52.44
annotatePeaks  49.44   0.20   49.64
GSCAplot       37.56   0.65   38.35
GSCAeda         6.82   0.03    8.33
* 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-3.2-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_1.8.0.zip
* DONE (GSCA)

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

nameusersystemelapsed
ConstructTG67.77 0.0267.79
GSCA154.24 3.43192.58
GSCAeda 7.00 0.0915.12
GSCAplot39.73 0.6440.76
GSCAui000
Oct4ESC_TG000
STAT1_TG0.020.000.02
annotatePeaks54.18 0.2560.46
geneIDdata0.110.000.11
tabSearch0.480.030.52

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

nameusersystemelapsed
ConstructTG52.40 0.0552.44
GSCA131.24 3.34145.24
GSCAeda6.820.038.33
GSCAplot37.56 0.6538.35
GSCAui0.020.000.01
Oct4ESC_TG000
STAT1_TG0.000.020.02
annotatePeaks49.44 0.2049.64
geneIDdata0.110.000.11
tabSearch0.600.030.64