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BioC 3.2: CHECK report for DeconRNASeq on moscato1

This page was generated on 2016-04-23 10:18:48 -0700 (Sat, 23 Apr 2016).

Package 257/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeconRNASeq 1.12.0
Ting Gong
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/DeconRNASeq
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: DeconRNASeq
Version: 1.12.0
Command: rm -rf DeconRNASeq.buildbin-libdir DeconRNASeq.Rcheck && mkdir DeconRNASeq.buildbin-libdir DeconRNASeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeconRNASeq.buildbin-libdir DeconRNASeq_1.12.0.tar.gz >DeconRNASeq.Rcheck\00install.out 2>&1 && cp DeconRNASeq.Rcheck\00install.out DeconRNASeq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DeconRNASeq.buildbin-libdir --install="check:DeconRNASeq-install.out" --force-multiarch --no-vignettes --timings DeconRNASeq_1.12.0.tar.gz
StartedAt: 2016-04-23 01:29:12 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:30:59 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 107.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DeconRNASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DeconRNASeq.buildbin-libdir DeconRNASeq.Rcheck && mkdir DeconRNASeq.buildbin-libdir DeconRNASeq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DeconRNASeq.buildbin-libdir DeconRNASeq_1.12.0.tar.gz >DeconRNASeq.Rcheck\00install.out 2>&1 && cp DeconRNASeq.Rcheck\00install.out DeconRNASeq-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DeconRNASeq.buildbin-libdir --install="check:DeconRNASeq-install.out" --force-multiarch --no-vignettes --timings DeconRNASeq_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/DeconRNASeq.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 'DeconRNASeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeconRNASeq' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'DeconRNASeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* 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' call to 'grid' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ggplot2' 'grid' 'pcaMethods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DeconRNASeq: no visible global function definition for 'prep'
DeconRNASeq: no visible global function definition for 'pca'
DeconRNASeq: no visible global function definition for 'R2cum'
DeconRNASeq: no visible global function definition for 'ggplot'
DeconRNASeq: no visible global function definition for 'aes'
DeconRNASeq: no visible global function definition for 'geom_point'
DeconRNASeq: no visible global function definition for 'labs'
DeconRNASeq: no visible global function definition for 'geom_abline'
DeconRNASeq: no visible global function definition for 'xlab'
DeconRNASeq: no visible global function definition for 'ylab'
multiplot: no visible global function definition for 'grid.newpage'
multiplot: no visible global function definition for 'pushViewport'
multiplot: no visible global function definition for 'viewport'
multiplot: no visible global function definition for 'grid.layout'
multiplot : vplayout: no visible global function definition for
  'viewport'
* 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' ... [7s] OK
** running examples for arch 'x64' ... [6s] OK
* 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/DeconRNASeq.Rcheck/00check.log'
for details.


DeconRNASeq.Rcheck/00install.out:


install for i386

* installing *source* package 'DeconRNASeq' ...
** R
** data
** demo
** 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 'DeconRNASeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeconRNASeq' as DeconRNASeq_1.12.0.zip
* DONE (DeconRNASeq)

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

nameusersystemelapsed
DeconRNASeq000
all.datasets0.230.010.25
array.proportions0.160.020.17
array.signatures0.070.020.10
condplot0.070.020.10
datasets0.20.00.2
fraction0.60.00.6
liver_kidney0.170.000.17
multi_tissue0.650.030.68
multiplot000
proportions0.160.010.17
signatures0.110.020.13
x.data0.40.00.4
x.signature0.460.000.45
x.signature.filtered0.530.010.55
x.signature.filtered.optimal0.710.000.71

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

nameusersystemelapsed
DeconRNASeq000
all.datasets0.090.010.11
array.proportions0.090.000.09
array.signatures0.170.000.17
condplot0.170.000.17
datasets0.160.000.16
fraction0.450.030.48
liver_kidney0.250.020.27
multi_tissue0.360.030.39
multiplot000
proportions0.110.000.11
signatures0.120.000.12
x.data0.410.000.41
x.signature0.350.020.36
x.signature.filtered0.290.000.30
x.signature.filtered.optimal0.550.010.56