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BioC 2.12: CHECK report for snm on moscato2

This page was generated on 2013-09-21 09:41:32 -0700 (Sat, 21 Sep 2013).

Package 605/671HostnameOS / ArchBUILDCHECKBUILD BIN
snm 1.8.0
Brig Mecham
Snapshot Date: 2013-09-20 17:00:50 -0700 (Fri, 20 Sep 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/snm
Last Changed Rev: 75263 / Revision: 80624
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: snm
Version: 1.8.0
Command: rm -rf snm.buildbin-libdir && mkdir snm.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=snm.buildbin-libdir snm_1.8.0.tar.gz >snm-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=snm.buildbin-libdir --install="check:snm-install.out" --force-multiarch --no-vignettes --timings snm_1.8.0.tar.gz && mv snm.buildbin-libdir/* snm.Rcheck/ && rmdir snm.buildbin-libdir
StartedAt: 2013-09-21 04:15:23 -0700 (Sat, 21 Sep 2013)
EndedAt: 2013-09-21 04:23:52 -0700 (Sat, 21 Sep 2013)
EllapsedTime: 509.0 seconds
RetCode: 0
Status:  OK  
CheckDir: snm.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/snm.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snm' version '1.8.0'
* 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 'snm' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcArrayEffects: warning in matrix(rff@ranef[offset:(-1 + offset +
  nrow(lf$FL$trms[[i]]$Zt))], nr = length(unique(snm.obj$int.var[,
  i]))): partial argument match of 'nr' to 'nrow'
fit.model: warning in matrix(0, nr = 1, nc = 1): partial argument match
  of 'nr' to 'nrow'
fit.model: warning in matrix(0, nr = 1, nc = 1): partial argument match
  of 'nc' to 'ncol'
fit.model: warning in matrix(rff@resid, nr = dim(Y.pooled)[1]): partial
  argument match of 'nr' to 'nrow'
sim.doubleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.doubleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.doubleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nr' to
  'nrow'
sim.doubleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nc' to
  'ncol'
sim.function.var: warning in matrix(0, nr = length(lab), nc = ncol(x)):
  partial argument match of 'nr' to 'nrow'
sim.function.var: warning in matrix(0, nr = length(lab), nc = ncol(x)):
  partial argument match of 'nc' to 'ncol'
sim.intensity.dep: warning in matrix(0, nr = ncol(x), nc = spline.dim):
  partial argument match of 'nr' to 'nrow'
sim.intensity.dep: warning in matrix(0, nr = ncol(x), nc = spline.dim):
  partial argument match of 'nc' to 'ncol'
sim.preProcessed: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.preProcessed: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.preProcessed: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nr' to
  'nrow'
sim.preProcessed: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nc' to
  'ncol'
sim.probe.specific: warning in matrix(0, nr = length(lab), nc =
  ncol(x)): partial argument match of 'nr' to 'nrow'
sim.probe.specific: warning in matrix(0, nr = length(lab), nc =
  ncol(x)): partial argument match of 'nc' to 'ncol'
sim.refDesign: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.refDesign: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.refDesign: warning in matrix(rnorm(length(M), 0, 0.25), nr =
  nrow(M), nc = ncol(M)): partial argument match of 'nr' to 'nrow'
sim.refDesign: warning in matrix(rnorm(length(M), 0, 0.25), nr =
  nrow(M), nc = ncol(M)): partial argument match of 'nc' to 'ncol'
sim.singleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.singleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.singleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nr' to
  'nrow'
sim.singleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nc' to
  'ncol'
snm.diagnostic.plot: warning in axis(side = 2, at = 500, label = "
  500+"): partial argument match of 'label' to 'labels'
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [186s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
snm              172.36   2.63  175.02
sim.preProcessed   5.91   0.09    6.01
** running examples for arch 'x64' ... [188s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
snm              170.21   3.60  174.14
sim.preProcessed   7.12   0.23    7.36
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/snm.Rcheck/00check.log'
for details.

snm.Rcheck/00install.out:


install for i386

* installing *source* package 'snm' ...
** R
** 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 'snm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snm' as snm_1.8.0.zip
* DONE (snm)