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BioC 3.0: CHECK report for SAGx on zin1

This page was generated on 2015-04-10 09:37:30 -0700 (Fri, 10 Apr 2015).

Package 796/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAGx 1.40.0
Per Broberg,
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SAGx
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: SAGx
Version: 1.40.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SAGx_1.40.0.tar.gz
StartedAt: 2015-04-10 04:09:56 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:10:39 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 43.3 seconds
RetCode: 0
Status:  OK 
CheckDir: SAGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SAGx_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SAGx.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAGx’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SAGx’ can be installed ... [3s/3s] 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
* 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 to packages already attached by Depends:
  ‘methods’ ‘stats’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘multtest’
  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
File ‘SAGx/R/internal.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

R2BASE: warning in write.table(next.line, file = out, se = "\t", append
  = TRUE, col.names = FALSE, row.names = FALSE, quote = FALSE): partial
  argument match of 'se' to 'sep'
plot,samroc.result-ANY : plot.samroc.result: warning in legend(x.coord,
  y.coord, legend = c("Observed statistic", "Null distribution"), col =
  c("red", "green"), lty = 1, cex = 0.8, y.int = 1): partial argument
  match of 'y.int' to 'y.intersp'
Fstat: no visible binding for global variable ‘M’
GSEA.mean.t: no visible binding for global variable ‘samroc.res’
GSEA.mean.t: no visible binding for global variable ‘kegg’
GSEA.mean.t : maxmeanf: no visible binding for global variable
  ‘plustat’
R2BASE: no visible binding for global variable ‘clingen’
R2BASE: no visible binding for global variable ‘AZID’
R2BASE: no visible binding for global variable ‘dats’
R2BASE: no visible binding for global variable ‘annots’
R2mim: no visible binding for global variable ‘inm’
Xprep: no visible binding for global variable ‘M’
Xprep.resid: no visible binding for global variable ‘M’
clin2mim: no visible binding for global variable ‘dbs’
clin2mim: no visible binding for global variable ‘clinical’
estimatep0: no visible binding for global variable ‘pp’
fetchSignal: no visible global function definition for ‘sqlQuery’
fp.fn: no visible binding for global variable ‘pvals’
gap: no visible binding for global variable ‘g’
list.experiments: no visible global function definition for ‘sqlQuery’
mat2TeX: no visible global function definition for ‘errif’
p0.mom: no visible binding for global variable ‘pvalues’
pava.fdr: no visible binding for global variable ‘pvalues’
rank.genes: no visible binding for global variable ‘indats’
rank.trend: no visible binding for global variable ‘x’
rsd.test: no visible binding for global variable ‘x’
rsd.test: no visible binding for global variable ‘y’
samrocN: no visible binding for global variable ‘M’
samrocNboot: no visible binding for global variable ‘M’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘SAGx/libs/SAGx.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘minigsea.o’, ‘newboot.o’, ‘samrocNboot.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/SAGx.Rcheck/00check.log’
for details.

SAGx.Rcheck/00install.out:

* installing *source* package ‘SAGx’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c minigsea.c -o minigsea.o
minigsea.c: In function ‘MiniGSEA’:
minigsea.c:8:12: warning: variable ‘k’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c newboot.c -o newboot.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c samrocNboot.c -o samrocNboot.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o SAGx.so minigsea.o newboot.o samrocNboot.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/SAGx.Rcheck/SAGx/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SAGx)

SAGx.Rcheck/SAGx-Ex.timings:

nameusersystemelapsed
Fstat0.0200.0000.023
JT.test0.0080.0000.008
fetchSignal0.0000.0000.001
firstpass0.0000.0000.001
gap1.6640.0001.668
list.experiments000
myclus1.5440.0001.544
outlier0.0000.0000.001
pava0.0000.0000.001
rank.trend0.0040.0000.002
samrocnboot3.7160.0323.765
union.of.pways000