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CHECK report for CSSP on merida2

This page was generated on 2018-10-17 08:51:46 -0400 (Wed, 17 Oct 2018).

Package 328/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSSP 1.18.0
Chandler Zuo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CSSP
Branch: RELEASE_3_7
Last Commit: acb4718
Last Changed Date: 2018-04-30 10:35:30 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CSSP
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CSSP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CSSP_1.18.0.tar.gz
StartedAt: 2018-10-16 20:45:29 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:46:29 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CSSP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CSSP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CSSP_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CSSP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSSP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSSP’ version ‘1.18.0’
* 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 ‘CSSP’ 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
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’ ‘utils’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.allFit: no visible global function definition for ‘quantile’
.allFit: no visible global function definition for ‘model.matrix’
.allFit: no visible global function definition for ‘glm’
.csspfit : pval.nb.cont.trunc: no visible global function definition
  for ‘runif’
.csspfit : pval.nb.cont.trunc: no visible global function definition
  for ‘pnbinom’
.csspfit : pval.nb.cont: no visible global function definition for
  ‘runif’
.csspfit : pval.nb.cont: no visible global function definition for
  ‘pnbinom’
.csspfit : pval.mod.w: no visible global function definition for
  ‘dnbinom’
.csspfit: no visible global function definition for ‘pnbinom’
.csspfit: no visible global function definition for ‘dnbinom’
.csspfit: no visible global function definition for ‘weighted.mean’
.csspfit: no visible global function definition for ‘na.omit’
.csspfit: no visible global function definition for ‘new’
.gridFit: no visible global function definition for ‘quantile’
.gridFit: no visible global function definition for ‘model.matrix’
.gridFit: no visible global function definition for ‘glm’
.gridFit: no visible global function definition for ‘predict.glm’
.nonpaFit: no visible global function definition for ‘quantile’
.nonpaFit: no visible global function definition for ‘weighted.mean’
createBinData: no visible global function definition for ‘read.table’
createBinData: no visible global function definition for ‘new’
createBinData: no visible global function definition for ‘na.omit’
readBinFile: no visible global function definition for ‘read.table’
callpeak,CSSPFit: no visible global function definition for ‘pnbinom’
callpeak,CSSPFit: no visible global function definition for ‘pgamma’
cssp.power,CSSPFit: no visible global function definition for ‘rgamma’
cssp.power,CSSPFit: no visible global function definition for ‘rbinom’
cssp.power,CSSPFit: no visible global function definition for ‘rpois’
cssp.power,CSSPFit: no visible global function definition for ‘pnbinom’
cssp.power,CSSPFit: no visible global function definition for ‘na.omit’
cssp.power,CSSPFit: no visible global function definition for ‘pgamma’
cssp.power,CSSPFit: no visible global function definition for ‘qnbinom’
cssp.power,CSSPFit: no visible global function definition for ‘qgamma’
cssp.power,CSSPFit: no visible global function definition for ‘runif’
cssp.power,CSSPFit: no visible global function definition for
  ‘weighted.mean’
cssp.sim,CSSPFit: no visible global function definition for ‘rgamma’
cssp.sim,CSSPFit: no visible global function definition for ‘rbinom’
cssp.sim,CSSPFit: no visible global function definition for ‘runif’
fit.freq,CSSPFit: no visible global function definition for ‘quantile’
fit.freq,CSSPFit : <anonymous>: no visible global function definition
  for ‘dnbinom’
pBBT,CSSPFit: no visible global function definition for ‘pgamma’
qBBT,CSSPFit: no visible global function definition for ‘quantile’
qBBT,CSSPFit: no visible global function definition for ‘uniroot’
show,CSSPFit: no visible global function definition for ‘showClass’
Undefined global functions or variables:
  dnbinom glm model.matrix na.omit new pgamma pnbinom predict.glm
  qgamma qnbinom quantile rbinom read.table rgamma rpois runif
  showClass uniroot weighted.mean
Consider adding
  importFrom("methods", "new", "showClass")
  importFrom("stats", "dnbinom", "glm", "model.matrix", "na.omit",
             "pgamma", "pnbinom", "predict.glm", "qgamma", "qnbinom",
             "quantile", "rbinom", "rgamma", "rpois", "runif", "uniroot",
             "weighted.mean")
  importFrom("utils", "read.table")
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 ... OK
* 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
cssp.power-methods 19.425  1.216  20.854
cssp.fit-methods    5.805  0.073   5.924
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_tests.R’
 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/CSSP.Rcheck/00check.log’
for details.



Installation output

CSSP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CSSP
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CSSP’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bincount.c -o bincount.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c binpower.c -o binpower.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridLogMean.c -o gridLogMean.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridMGC.c -o gridMGC.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridMean.c -o gridMean.o
gridMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
                                                              ^
gridMean.c:177:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
                                                              ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridMode.c -o gridMode.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridNonpa.c -o gridNonpa.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridSample.c -o gridSample.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tag2bin.c -o tag2bin.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 CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/CSSP/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
* DONE (CSSP)

Tests output

CSSP.Rcheck/tests/run_tests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # --------------------------------------------------------------
> #  2011 Winged Foot Capital Research, LLC - All rights reserved
> # author: Suraj Gupta <suraj@wingedfootcapital.com>
> # --------------------------------------------------------------
> 
> library( "testthat" )
> 
> # convert all warnings to errors
> options( warn = 1 )
> 
> # run tests
> # test_package( "CSSP" )
> test_check( "CSSP" )
Loading required package: CSSP
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 62 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.691   0.225   3.921 

Example timings

CSSP.Rcheck/CSSP-Ex.timings

nameusersystemelapsed
CSSPFit-class0.0020.0010.003
bindcount0.1350.0090.146
bindcount.chr0.0210.0030.024
callpeak-methods0.0100.0020.012
createBinData0.3190.0210.340
cssp.fit-methods5.8050.0735.924
cssp.power-methods19.425 1.21620.854
cssp.sim-methods0.0220.0100.032
fit.freq-methods0.2150.0160.236
pBBT-methods0.0080.0010.010
peakcount0.1150.0060.123
peakcount.chr0.0150.0020.017
qBBT-methods0.0350.0020.037
readBinFile0.0190.0030.022
tag2bin0.0140.0060.021
tag2bin.chr0.0070.0010.009