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CHECK report for SSPA on celaya2

This page was generated on 2019-10-16 12:47:30 -0400 (Wed, 16 Oct 2019).

Package 1588/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SSPA 2.24.0
Maarten van Iterson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SSPA
Branch: RELEASE_3_9
Last Commit: 879667c
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SSPA
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SSPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SSPA_2.24.0.tar.gz
StartedAt: 2019-10-16 07:09:08 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:10:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 75.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SSPA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SSPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SSPA_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SSPA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SSPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SSPA’ version ‘2.24.0’
* 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 ‘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
* 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 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 : : 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 : : 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 : : no visible global function definition
  for ‘dnorm’
df0,Distribution : : no visible global function definition
  for ‘dt’
df0,Distribution : : no visible global function definition
  for ‘df’
df0,Distribution : : no visible global function definition
  for ‘dchisq’
df1,Distribution : : no visible global function definition
  for ‘dnorm’
df1,Distribution : : no visible global function definition
  for ‘dt’
df1,Distribution : : no visible global function definition
  for ‘df’
df1,Distribution : : no visible global function definition
  for ‘dchisq’
pf0,Distribution : : no visible global function definition
  for ‘pnorm’
pf0,Distribution : : no visible global function definition
  for ‘pt’
pf0,Distribution : : no visible global function definition
  for ‘pf’
pf0,Distribution : : no visible global function definition
  for ‘pchisq’
pf1,Distribution : : no visible global function definition
  for ‘pnorm’
pf1,Distribution : : no visible global function definition
  for ‘pt’
pf1,Distribution : : no visible global function definition
  for ‘pf’
pf1,Distribution : : no visible global function definition
  for ‘pchisq’
plot,PilotData : : no visible global function definition for
  ‘panel.histogram’
plot,PilotData : : no visible global function definition for
  ‘panel.xyplot’
plot,PilotData : : no visible global function definition for
  ‘panel.abline’
plot,PilotData: no visible binding for global variable
  ‘prepanel.qqmathline’
plot,PilotData : : no visible global function definition for
  ‘panel.qqmathline’
plot,PilotData : : no visible global function definition for
  ‘panel.qqmath’
qf0,Distribution : : no visible global function definition
  for ‘qnorm’
qf0,Distribution : : no visible global function definition
  for ‘qt’
qf0,Distribution : : no visible global function definition
  for ‘qf’
qf0,Distribution : : 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
sampleSize 9.132  1.188  10.322
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SSPA.Rcheck/00check.log’
for details.

Installation output

SSPA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SSPA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SSPA’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
Rinit.c:11:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  NULL
  ^~~~
  {   }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^~~~~~~~~~
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c massdist.c -o massdist.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nncg.c -o nncg.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SSPA.so Rinit.o massdist.o nncg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-SSPA/00new/SSPA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SSPA)

Tests output

Example timings

SSPA.Rcheck/SSPA-Ex.timings

nameusersystemelapsed
Nutrigenomics0.0500.0090.059
dbitri0.0040.0010.005
deepSAGE0.0340.0080.042
pbitri0.0360.0030.039
pilotData0.3620.0070.369
qbitri0.0040.0010.004
rbitri0.0030.0000.004
sampleSize 9.132 1.18810.322
simdat0.0410.0040.046