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BioC 3.4: CHECK report for SSPA on tokay1

This page was generated on 2017-04-15 16:15:54 -0400 (Sat, 15 Apr 2017).

Package 1196/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SSPA 2.14.0
Maarten van Iterson
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/SSPA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SSPA
Version: 2.14.0
Command: rm -rf SSPA.buildbin-libdir SSPA.Rcheck && mkdir SSPA.buildbin-libdir SSPA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SSPA.buildbin-libdir SSPA_2.14.0.tar.gz >SSPA.Rcheck\00install.out 2>&1 && cp SSPA.Rcheck\00install.out SSPA-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SSPA.buildbin-libdir --install="check:SSPA-install.out" --force-multiarch --no-vignettes --timings SSPA_2.14.0.tar.gz
StartedAt: 2017-04-15 01:01:47 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:02:50 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 62.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SSPA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SSPA.buildbin-libdir SSPA.Rcheck && mkdir SSPA.buildbin-libdir SSPA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SSPA.buildbin-libdir SSPA_2.14.0.tar.gz >SSPA.Rcheck\00install.out 2>&1 && cp SSPA.Rcheck\00install.out SSPA-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SSPA.buildbin-libdir --install="check:SSPA-install.out" --force-multiarch --no-vignettes --timings SSPA_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/SSPA.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SSPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SSPA' version '2.14.0'
* 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 'SSPA' 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
Package in Depends field not imported from: 'methods'
  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
Dn: no visible global function definition for 'points'
Gnhat: no visible global function definition for 'qnorm'
Gnhat : <anonymous>: no visible global function definition for 'pnorm'
Hntilde: no visible global function definition for 'dbinom'
deconvolution: no visible global function definition for 'approx'
findroot: no visible global function definition for 'curve'
findroot: no visible global function definition for 'grid'
findroot: no visible global function definition for 'abline'
picardplot: no visible global function definition for 'points'
picardplot: no visible global function definition for 'abline'
pilotData: no visible global function definition for 'new'
qbitri: no visible global function definition for 'runif'
rbitri: no visible global function definition for 'runif'
regularization: no visible global function definition for 'points'
regularization: no visible global function definition for 'par'
sampleSize: no visible global function definition for 'new'
simdat : <anonymous>: no visible global function definition for 'rnorm'
simdat: no visible global function definition for 'rnorm'
trimbin: no visible global function definition for 'quantile'
trimbin: no visible global function definition for 'hist'
trimbin: no visible global function definition for 'ecdf'
df0,Distribution : <anonymous>: no visible global function definition
  for 'dnorm'
df0,Distribution : <anonymous>: no visible global function definition
  for 'dt'
df0,Distribution : <anonymous>: no visible global function definition
  for 'df'
df0,Distribution : <anonymous>: no visible global function definition
  for 'dchisq'
df1,Distribution : <anonymous>: no visible global function definition
  for 'dnorm'
df1,Distribution : <anonymous>: no visible global function definition
  for 'dt'
df1,Distribution : <anonymous>: no visible global function definition
  for 'df'
df1,Distribution : <anonymous>: no visible global function definition
  for 'dchisq'
pf0,Distribution : <anonymous>: no visible global function definition
  for 'pnorm'
pf0,Distribution : <anonymous>: no visible global function definition
  for 'pt'
pf0,Distribution : <anonymous>: no visible global function definition
  for 'pf'
pf0,Distribution : <anonymous>: no visible global function definition
  for 'pchisq'
pf1,Distribution : <anonymous>: no visible global function definition
  for 'pnorm'
pf1,Distribution : <anonymous>: no visible global function definition
  for 'pt'
pf1,Distribution : <anonymous>: no visible global function definition
  for 'pf'
pf1,Distribution : <anonymous>: no visible global function definition
  for 'pchisq'
plot,PilotData : <anonymous>: no visible global function definition for
  'panel.histogram'
plot,PilotData : <anonymous>: no visible global function definition for
  'panel.xyplot'
plot,PilotData : <anonymous>: no visible global function definition for
  'panel.abline'
plot,PilotData: no visible binding for global variable
  'prepanel.qqmathline'
plot,PilotData : <anonymous>: no visible global function definition for
  'panel.qqmathline'
plot,PilotData : <anonymous>: no visible global function definition for
  'panel.qqmath'
qf0,Distribution : <anonymous>: no visible global function definition
  for 'qnorm'
qf0,Distribution : <anonymous>: no visible global function definition
  for 'qt'
qf0,Distribution : <anonymous>: no visible global function definition
  for 'qf'
qf0,Distribution : <anonymous>: no visible global function definition
  for 'qchisq'
show,PilotData: no visible global function definition for 'str'
show,SampleSize: no visible global function definition for 'str'
Undefined global functions or variables:
  abline approx curve dbinom dchisq df dnorm dt ecdf grid hist new
  panel.abline panel.histogram panel.qqmath panel.qqmathline
  panel.xyplot par pchisq pf pnorm points prepanel.qqmathline pt qchisq
  qf qnorm qt quantile rnorm runif str
Consider adding
  importFrom("graphics", "abline", "curve", "grid", "hist", "par",
             "points")
  importFrom("methods", "new")
  importFrom("stats", "approx", "dbinom", "dchisq", "df", "dnorm", "dt",
             "ecdf", "pchisq", "pf", "pnorm", "pt", "qchisq", "qf",
             "qnorm", "qt", "quantile", "rnorm", "runif")
  importFrom("utils", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/SSPA.buildbin-libdir/SSPA/libs/i386/SSPA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
sampleSize 5.71   0.05    5.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
sampleSize  5.4   0.11    5.51
* 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

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/SSPA.Rcheck/00check.log'
for details.

SSPA.Rcheck/00install.out:


install for i386

* installing *source* package 'SSPA' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
Rinit.c:12:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
Rinit.c:12:1: warning: (near initialization for 'cMethods[2]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c massdist.c -o massdist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c nncg.c -o nncg.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SSPA.dll tmp.def Rinit.o massdist.o nncg.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/SSPA.buildbin-libdir/SSPA/libs/i386
** R
** data
** 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 'SSPA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Rinit.c -o Rinit.o
Rinit.c:12:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
Rinit.c:12:1: warning: (near initialization for 'cMethods[2]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c massdist.c -o massdist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nncg.c -o nncg.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SSPA.dll tmp.def Rinit.o massdist.o nncg.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/SSPA.buildbin-libdir/SSPA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SSPA' as SSPA_2.14.0.zip
* DONE (SSPA)

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

nameusersystemelapsed
Nutrigenomics0.030.000.04
dbitri000
deepSAGE0.040.000.04
pbitri000
pilotData0.220.000.22
qbitri000
rbitri0.000.010.02
sampleSize5.710.055.75
simdat0.060.000.06

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

nameusersystemelapsed
Nutrigenomics0.020.010.03
dbitri000
deepSAGE0.030.000.03
pbitri000
pilotData0.290.000.29
qbitri000
rbitri000
sampleSize5.400.115.51
simdat0.050.000.05