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BioC 2.12: CHECK report for SAGx on george2

This page was generated on 2013-10-09 09:37:21 -0700 (Wed, 09 Oct 2013).

Package 581/671HostnameOS / ArchBUILDCHECKBUILD BIN
SAGx 1.34.0
Per Broberg,
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/SAGx
Last Changed Rev: 75263 / Revision: 81334
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: SAGx
Version: 1.34.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SAGx_1.34.0.tar.gz
StartedAt: 2013-10-09 04:51:46 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:53:25 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 99.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SAGx.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SAGx.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.34.0’
* 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 ... [7s/7s] 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
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 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 ... [21s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
samrocnboot 11.929  0.112  12.406
* 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/SAGx.Rcheck/00check.log’
for details.

SAGx.Rcheck/00install.out:

* installing *source* package ‘SAGx’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-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-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c samrocNboot.c -o samrocNboot.o
gcc -std=gnu99 -shared -L/usr/local/lib -o SAGx.so minigsea.o newboot.o samrocNboot.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
Fstat0.1080.0040.128
JT.test0.0280.0000.029
fetchSignal0.0200.0000.033
firstpass0.0200.0000.025
gap3.180.023.58
list.experiments0.0120.0000.012
myclus2.8440.0083.072
outlier0.0160.0000.017
pava0.0120.0000.014
rank.trend0.0240.0000.022
samrocnboot11.929 0.11212.406
union.of.pways0.0120.0000.011