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Package 585/658HostnameOS / ArchBUILDCHECKBUILD BIN
SIM 1.29.2
Renee X. de Menezes
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SIM
Last Changed Rev: 73101 / Revision: 74774
Last Changed Date: 2013-02-03 03:34:41 -0800 (Sun, 03 Feb 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 Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: SIM
Version: 1.29.2
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SIM_1.29.2.tar.gz
StartedAt: 2013-03-25 04:40:10 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:44:23 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 252.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SIM.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIM’ version ‘1.29.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SIM’ can be installed ... [20s/21s] 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
* 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
File ‘SIM/R/zzz.R’:
  .onAttach calls:
    library.dynam("SIM", pkg, lib)

See section ‘Good practice’ in '?.onAttach'.

dependent.heatmap: warning in get(as.character(adjust[[2]]), env =
  attr(adjust, ".Environment")): partial argument match of 'env' to
  'envir'
sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")):
  partial argument match of 'env' to 'envir'
sim.update.chrom.table: warning in factor(table$name, level = c(1:22,
  "X", "Y")): partial argument match of 'level' to 'levels'
assemble.data: no visible binding for global variable ‘chrom.table’
convertGenomicRegion: no visible binding for global variable
  ‘chrom.table’
link.metadata: no visible binding for global variable ‘expr.data’
link.metadata: no visible binding for global variable ‘hgu133plus2CHR’
link.metadata: no visible binding for global variable
  ‘hgu133plus2CHRLOC’
link.metadata: no visible binding for global variable
  ‘hgu133plus2SYMBOL’
plotCytobands: no visible binding for global variable ‘chrom.table’
sim.plot.pvals.on.genome: no visible binding for global variable
  ‘chrom.table’
sim.update.chrom.table: no visible global function definition for
  ‘dbConnect’
sim.update.chrom.table: no visible global function definition for
  ‘MySQL’
sim.update.chrom.table: no visible global function definition for
  ‘dbGetQuery’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
SIM-package         21.205  0.140  21.377
integrated.analysis 17.882  0.016  18.044
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/SIM.Rcheck/00check.log’
for details.

SIM.Rcheck/00install.out:

* installing *source* package ‘SIM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c withinWindow.c -o withinWindow.o
gcc -std=gnu99 -shared -L/usr/local/lib -o SIM.so withinWindow.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/SIM.Rcheck/SIM/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘SIM.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded
* DONE (SIM)

SIM.Rcheck/SIM-Ex.timings:

nameusersystemelapsed
RESOURCERER.annotation.to.ID0.0160.0000.017
SIM-package21.205 0.14021.377
acgh.data0.0160.0000.014
assemble.data0.0880.0000.086
chrom.table0.0240.0040.026
expr.data0.0280.0000.026
getoverlappingregions0.5480.0000.548
impute.nas.by.surrounding0.0080.0000.006
integrated.analysis17.882 0.01618.044
link.metadata0.0280.0000.028
samples0.0200.0000.019
sim.plot.overlapping.indep.dep.features0.1720.0080.177
sim.plot.pvals.on.genome0.4800.0600.539
sim.plot.pvals.on.region0.0400.0080.046
sim.plot.zoom.in0.5640.0200.586
sim.plot.zscore.heatmap1.4120.0241.434
sim.update.chrom.table0.0120.0000.012
tabulate.pvals0.0360.0000.038
tabulate.top.dep.features0.0680.0000.071
tabulate.top.indep.features0.0680.0000.070