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BioC 3.0: CHECK report for SAGx on moscato1

This page was generated on 2015-04-10 09:44:26 -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: rm -rf SAGx.buildbin-libdir SAGx.Rcheck && mkdir SAGx.buildbin-libdir SAGx.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SAGx.buildbin-libdir SAGx_1.40.0.tar.gz >SAGx.Rcheck\00install.out 2>&1 && cp SAGx.Rcheck\00install.out SAGx-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=SAGx.buildbin-libdir --install="check:SAGx-install.out" --force-multiarch --no-vignettes --timings SAGx_1.40.0.tar.gz
StartedAt: 2015-04-10 05:23:52 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:25:23 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 90.6 seconds
RetCode: 0
Status:  OK  
CheckDir: SAGx.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf SAGx.buildbin-libdir SAGx.Rcheck && mkdir SAGx.buildbin-libdir SAGx.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SAGx.buildbin-libdir SAGx_1.40.0.tar.gz >SAGx.Rcheck\00install.out 2>&1 && cp SAGx.Rcheck\00install.out SAGx-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=SAGx.buildbin-libdir --install="check:SAGx-install.out" --force-multiarch --no-vignettes --timings SAGx_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/SAGx.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'SAGx' can be installed ... 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
* 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' 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/SAGx.buildbin-libdir/SAGx/libs/i386/SAGx.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.0-bioc/meat/SAGx.buildbin-libdir/SAGx/libs/x64/SAGx.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)

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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [11s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
samrocnboot 5.27   0.25    5.52
* 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
  'D:/biocbld/bbs-3.0-bioc/meat/SAGx.Rcheck/00check.log'
for details.

SAGx.Rcheck/00install.out:


install for i386

* installing *source* package 'SAGx' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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 -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c newboot.c -o newboot.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c samrocNboot.c -o samrocNboot.o
gcc -m32 -shared -s -static-libgcc -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/SAGx.buildbin-libdir/SAGx/libs/i386
** 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 'SAGx' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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 -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c newboot.c -o newboot.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c samrocNboot.c -o samrocNboot.o
gcc -m64 -shared -s -static-libgcc -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/SAGx.buildbin-libdir/SAGx/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAGx' as SAGx_1.40.0.zip
* DONE (SAGx)

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

nameusersystemelapsed
Fstat0.020.000.02
JT.test0.010.000.01
fetchSignal000
firstpass000
gap1.630.001.63
list.experiments000
myclus1.620.001.62
outlier000
pava000
rank.trend000
samrocnboot4.260.114.37
union.of.pways000

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

nameusersystemelapsed
Fstat0.000.010.02
JT.test0.010.000.01
fetchSignal000
firstpass000
gap1.890.021.91
list.experiments000
myclus1.890.001.89
outlier000
pava000
rank.trend000
samrocnboot5.270.255.52
union.of.pways0.010.000.02