Package: CSSP

Version: 1.22.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSSP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CSSP_1.22.0.tar.gz

StartedAt: 2019-10-16 03:00:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:02:12 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 98.1 seconds

RetCode: 0

Status:  OK

CheckDir: CSSP.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSSP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CSSP_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CSSP.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CSSP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSSP' version '1.22.0'
* 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 '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
* 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
* 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 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 : : 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 ... NOTE
File 'CSSP/libs/i386/CSSP.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gridSample.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gridSample.o'
File 'CSSP/libs/x64/CSSP.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gridSample.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gridSample.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
cssp.power-methods 25.27   0.52   25.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
cssp.power-methods 17.75   0.36   18.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_tests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/CSSP.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CSSP_1.22.0.tar.gz && rm -rf CSSP.buildbin-libdir && mkdir CSSP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CSSP.buildbin-libdir CSSP_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CSSP_1.22.0.zip && rm CSSP_1.22.0.tar.gz CSSP_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  413k  100  413k    0     0  1336k      0 --:--:-- --:--:-- --:--:-- 1369k

install for i386

* installing *source* package 'CSSP' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bincount.c -o bincount.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c binpower.c -o binpower.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gridLogMean.c -o gridLogMean.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gridMGC.c -o gridMGC.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gridMean.c -o gridMean.o
gridMean.c: In function 'gridMGCmean_c':
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: In function 'gridMmean_c':
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;
                                                               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gridMode.c -o gridMode.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gridNonpa.c -o gridNonpa.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gridSample.c -o gridSample.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c tag2bin.c -o tag2bin.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o CSSP.dll tmp.def bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CSSP.buildbin-libdir/00LOCK-CSSP/00new/CSSP/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CSSP'
    finding HTML links ... done
    BinData-class                           html  
    CSSPFit-class                           html  
    bin.data                                html  
    bindata.chr1                            html  
    bindcount                               html  
    bindcount.chr                           html  
    bindpos                                 html  
    callpeak-methods                        html  
    createBinData                           html  
    cssp.fit-methods                        html  
    cssp.power-methods                      html  
    cssp.sim-methods                        html  
    fit.freq-methods                        html  
    pBBT-methods                            html  
    peakcount                               html  
    peakcount.chr                           html  
    peakpos                                 html  
    qBBT-methods                            html  
    readBinFile                             html  
    sampleFit                               html  
    tag2bin                                 html  
    tag2bin.chr                             html  
    tagdat_chip                             html  
    tagdat_input                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CSSP' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bincount.c -o bincount.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c binpower.c -o binpower.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gridLogMean.c -o gridLogMean.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gridMGC.c -o gridMGC.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gridMean.c -o gridMean.o
gridMean.c: In function 'gridMGCmean_c':
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: In function 'gridMmean_c':
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;
                                                               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gridMode.c -o gridMode.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gridNonpa.c -o gridNonpa.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gridSample.c -o gridSample.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tag2bin.c -o tag2bin.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o CSSP.dll tmp.def bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CSSP.buildbin-libdir/CSSP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSSP' as CSSP_1.22.0.zip
* DONE (CSSP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CSSP' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
> # --------------------------------------------------------------
> 
> 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: 56 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   2.92    0.26    3.23 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
> # --------------------------------------------------------------
> 
> 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: 56 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.00    0.14    3.18